Skip to content

1.2 Single locus

tresor.locus.library is the module that can simulate sequencing libraries at a given single locus. A single genomic locus represents where a genome segment is fragmented into pieces for sequencing, irrespective of information on specific genes and cells. Therefore, this can be treated as a baseline to validate users' hypotheses and evaluate tool performance.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
import tresor as ts

ts.locus.library(
    seq_num=50,
    len_params={
        'umi': {
            'umi_unit_pattern': 2,
            'umi_unit_len': 12,
        },
    },
    seq_params={
        'custom': 'AAGC',  # BAGC
        'custom_1': 'V',
    },
    material_params={
        'fasta_cdna_fpn': to('data/Homo_sapiens.GRCh38.cdna.all.fa.gz'),  # None False
    },
    is_seed=True,

    working_dir=to('data/simu/docs/'),

    condis=['umi', 'custom', 'seq', 'custom_1'],
    sim_thres=3,
    permutation=0,

    mode='short_read',  # long_read short_read

    verbose=True,  # False True
)

1
2
3
4
5
6
7
8
9
tresor library_sl \
-cfpn ./tresor/data/libslocus.yml \
-snum 50 \
-permut 0 \
-sthres 3 \
-wd ./tresor/data/simu/ \
-md short_read \
-is True \
-vb True

Attributes

Illustration

Attribute Description
seq_num number of RNA molecules. 50 by default
len_params lengths of different components of a read
seq_params sequences of different components of a read, It allows users to add their customised sequences
material_params a Python dictionary. Showing if cDNA libraries are provided, please use key word fasta_cdna_fpn. The human cDNA library can be downloaded through the Ensembl genome database
is_seed if seeds are used to simulate sequencing libraries. This is designed to make in silico experiments reproducible
working_dir working directory where all simulation results are about to be saved
condis names of components that a read contains. It can contains an unlimited number of read components
sim_thres similarity threshold. 3 by default
permutation permutation times
mode long_read or short_read
verbose whether to print intermediate results
Attribute Description
cfpn location to the yaml configuration file. Users can specify the atrributes illustrated on the Python tab in the .yml file.
snum number of sequencing molecules
permut permutation times
sthres similarity threshold. 3 by default
wd working directory where all simulation results are about to be saved
md long_read or short_read mode
is if seeds are used to simulate sequencing libraries. This is designed for reproducible in silico experiments
vb whether to print intermediate results

```

Extension

Tip

We can flexibly design the structure of a read by adding different components to condis separated by comma. For example, there is an initial read containing only a UMI. 

condis=['umi'],

Next, we can add a seq next to it. 

condis=['umi', 'seq'],

If we have a read containing many bespoke parts, primer, primer_1, spacer, spacer_1, adapter, adapter_1,umi, umi_1, 'seq', and 'seq_2', we can set condis just as 

condis=['umi', 'primer', 'primer_1', 'spacer', 'spacer_1', 'adapter', 'adapter_1', 'seq', 'seq_2', 'umi_1'],

Then, we can add the corresponding lengths of the parts/components in len_params as follows. 

len_params={
    'umi': {
        'umi_unit_pattern': 3,
        'umi_unit_len': 12,
    },
    'umi_1': {
        'umi_unit_pattern': 3,
        'umi_unit_len': 12,
    },
    'seq': 100,
    'seq_2': 100,
    'adapter': 10,
    'adapter_1': 10,
    'primer': 10,
    'primer_1': 10,
    'spacer': 10,
    'spacer_1': 10,
},

If you have known sequences of some components in read 1, you can use seq_params to specify customed sequences. The following settings were used in our recently released biotechnology, anchor-enhanced technology, for elevating the discovery of long-reads. We placed an anchor sequence BAGC and a V base in between the read 1 sequence where B means any type of a base. Tresor was used for simulating reads with the two custom sequences placed as follows. 

seq_params={
    'custom': 'AAGC',  # BAGC
    'custom_1': 'V',
},

Output

Console

D:\Programming\anaconda3\envs\umi\python.exe D:\Document\Programming\Python\tresor\tresor\locus.py 
17/07/2024 14:04:15 logger: Initialisation and parameters: 
{'seq_params': {'custom': 'AAGC', 'custom_1': 'V'}, 'material_params': {'fasta_cdna_fpn': 'D:\\Document\\Programming\\Python\\tresor\\tresor\\data/Homo_sapiens.GRCh38.cdna.all.fa.gz'}, 'mode': 'short_read', 'bead_mutation': True, 'bead_mut_rate': 0.0001, 'bead_deletion': True, 'bead_del_rate': 0.016, 'bead_insertion': True, 'bead_ins_rate': 7.1e-07}
17/07/2024 14:04:15 logger: ======>Sequencing library preparation starts
17/07/2024 14:04:15 logger: ======>Condition map: {'umi': ['alone'], 'custom': ['alone', '1'], 'seq': ['alone']}
17/07/2024 14:04:15 logger: ======>Read CDNAs from a reference ome
17/07/2024 14:04:21 logger: ======>There are 204083 genes in the reference genome
17/07/2024 14:04:21 logger: ======>Read 1 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGAAATTTAAACCCTTTAAAGGGAAAAAAGGGCCC', 'seq': 'GGTATGAAGACACAGGGAGACGTCGGGCCACAAGGGAACCCACTGAGGTGGGGACCAAAGATGGTGGCTCTTTGAATTGGAGCCAAGCGTGGTGGGCACC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 2 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGTTTAAACCCCCCCCCGGGAAATTTTTTGGGTTT', 'seq': 'CCTCCCCAGGATCTCGGACCAGCCCTCAGGAGCTGTCAGAGGAACTAAGCAGAAGGCTTCAGATCACTCCAGACTCCAATGGGGAACAGTTCAGCTCTTT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 3 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAATTTGGGCCCGGGAAAGGGCCCAAAAAAGGGAAA', 'seq': 'AAGTCATATGGGGATAGCAGGAGCAAGAGAGAGAGGAGGTGGCAGGCTCTAAACAACCAGCTCTGGCATGAACTAACAGTGAGAACTCATTATTTACCAT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 4 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCAAAAAAGGGGGGCCCCCCCCCGGGAAAGGGAAA', 'seq': 'CAGCGACTCTGCCAGCTCAAGGGACCCACCTGCCAGTACAGGGCAGCCCAATCTGGTCCCTCTGAACGGCCAGGACCTCCGCAGAGGGCCCTGCTGGCAC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 5 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTCCCGGGCCCGGGAAAGGGAAAGGGTTTGGGGGG', 'seq': 'CCCTTTGGGTTTAGCACGATGAGCTCAATCGGCACTGGGTATGACCTGTCAGCCTCTACATTCTCTCCTGACGGAAGAGTTTTTCAAGTTGAATATGCTA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 6 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAACCCGGGTTTCCCCCCGGGCCCCCCGGGCCCAAA', 'seq': 'GAAAATCAAGATGAAATAGAAAATATGATGAATGCAATATTTAAAGGAGTGTTTGTACATAGATACCGTGATGCGATAGCTGAAATTCGAGCTATTTGCA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 7 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAACCCAAAAAACCCTTTCCCAAACCCGGGGGGTTT', 'seq': 'CACTTCCAAATTTGAGATGTAGGCATTTCTGCCTCAACTTGCTAGCTGCGATTTTAAAAGCTTATGTTCCTGAGGAAGAATTGAAGGCAGCAGAAATAGA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 8 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCAAACCCAAAGGGCCCAAAGGGGGGAAACCCCCC', 'seq': 'CAAGAGGGACCCCAGAAACTGATCCGCAAAGTGTCTACCTCGGGGCAGATCCGGACCAAGACCAGTATTAAAGAGGGACAGCTATTGAAGCAAACCAGTT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 9 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTCCCAAAGGGAAAGGGTTTGGGAAACCCTTTAAA', 'seq': 'ATCTATCCAGGGAGGGGGAGGCCCATGAACGTAGGTTCTCTGCAGGGCCCAAGGTCAACGGAACATTCCAGGCTGACTTTCCTCTGGGCCCTGCCACCCA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 10 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCTTTCCCCCCTTTTTTTTTCCCTTTTTTTTTGGG', 'seq': 'TCCCCTTCAGGGACGTGAGCATCTAGCTGCACTGATTTGTTGTTCAGGAACAGGAAATGAAACCCCGCAGCTTTGAACACAATAACCCACGCCAGCCTCA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 11 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGCCCAAACCCGGGAAATTTCCCAAACCCGGGCCC', 'seq': 'GGGAAGATTGGGGCCTTCTGATTATTTTGGTGAAATTGCACTACTGATGAATCGTCCTCGTGCTGCCACAGTTGTTGCTCGTGGCCCCTTGAAGTGCGTT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 12 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGTTTGGGCCCTTTGGGGGGAAATTTTTTGGGCCC', 'seq': 'GGCCAGGCGCCTTCTGGACACCGTCTGGAATAAGGGTACTTGGGCCTGTCAGAAGCTCATCGCGGCTGCCCAAGAAGCCCAGGCCGACAGCCAGTCCCCC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 13 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAAGGGCCCTTTTTTCCCTTTAAACCCCCCCCCAAA', 'seq': 'GGTGAACAGGCGACCATGCTTTTCAGCTCTGGAAGTCGATGAAACATACGTTCCCAAAGAGTTTAATGCTGAAACATTCACCTTCCATGCAGATATATGC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 14 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCAAATTTTTTAAAGGGTTTGGGCCCGGGGGGGGG', 'seq': 'CACATTGTCATATGCTAGTGATCTCTATAATGGTTCCAGTATAGTCTCTAGTATTGAATTTGACCGGGATTGTGACTATTTTGCGATTGCTGGAGTTACA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': False}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 15 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGCCCAAAGGGGGGGGGGGGTTTGGGGGGTTTCCC', 'seq': 'ACTCCAGCCTGGGTGACAAAGTGAGACTCCGTCACAACAACAACAACAAAAAGCTTCCCCAACTAAAGCCTAGAAGAGCTTCTGAGGCGCTGCTTTGTCA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 16 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCAAATTTTTTTTTAAAGGGGGGCCCCCCCCCGGG', 'seq': 'AGACCCCTTGACATCAAGCTCTCTGGGAAGTGGAGCACTGATGATATGCAGATCAATGGCATTTCCCTGCAGGATTACACTGCAGTGAAGGAGAAGTATG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 17 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGGGGTTTGGGAAAAAAGGGTTTCCCGGGGGGCCC', 'seq': 'CATTAAAAAGGGTCTTGCTGCAAAGAGAAAAAGGATTGAAAGCGTTGCAAAAGCTTGCAACGAAACAAACAACAAAATTAAACGTATTTTGAGAACAATA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 18 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTCCCGGGAAAAAATTTTTTCCCAAAGGGCCCCCC', 'seq': 'GAAGCCCGCCGCCTCCCCGCGGCCCCGGCGAGCAGCCGCCGCCCGCCGCACCCATGAGCATGTCAGTGAAAAAACCAGTGAATCGCCTTCCAAACCAGGA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 19 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAATTTGGGCCCCCCAAACCCCCCTTTGGGGGGAAA', 'seq': 'AGACTAGGCGATCCTCACTTCTACCAGGACTCTTTGTGGCTGCGCAAGGAGTTCATGCAAGTTCGAAGGTGACCTCTTGTCACACTGATGGATACTTTTC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 20 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGGGGCCCAAAAAAAAACCCGGGGGGGGGAAAGGG', 'seq': 'TGGAGGCCGCGGACATTTTGGTGCCAAGCCGAACCGAGCCGGGGCGCCGGGAGCTATTGGGACCTGCGGCCTGGCTACAGATAAGGGACCAAAATGACTG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 21 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTTTTTTTGGGCCCGGGAAAAAACCCAAAGGGGGG', 'seq': 'TCTCCTCGTCGTCCTCCGGAGCCGAGACGTCCGCATCCGGCGGCAGCGGAAGCCCAGGAGCCTGCCCTGCCCTGGGGACGAAGAGCTGCAGCTCCTCCTG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 22 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAATTTGGGGGGAAACCCTTTTTTCCCGGGCCCCCC', 'seq': 'CCAATGGTCTATCAGGAAGTAGAAGAGCAGATCCAAACGATCAAAGATGTTGCTGGAGATAAATAGGCAGAAGGAAGAAGAGGACCTCAAATTACAATTG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 23 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAATTTTTTAAACCCAAAAAAAAAAAATTTTTTCCC', 'seq': 'TTCAGCAGTTGCCTCAATTAAGGCCTTGGAACCAGGGAGTGAAAAAAATAGATCCTGATTTATATGAAAAGTTTATCAGTCACAGATTTGGAGAAGAAAT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': False}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 24 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCCCCGGGGGGAAAAAATTTCCCTTTGGGAAACCC', 'seq': 'CTGGCATCGGCTAGTGGGTCAGTGTGGATGGCGGGGGCGGGGTATGAGCTAGTCCTCTGTCTCCCACCAGATGTGCTGTGATCACCGAGTTTGCTCGCAT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 25 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGTTTTTTCCCTTTCCCAAAGGGCCCGGGCCCGGG', 'seq': 'CTCTCCCCGGCCCCACTCGCCAGGTCCTACCACGATGCCTGACTCGTTTGCGGCTTTGGGACCGGTTGTAGGTGGCTTGACCGTCACTAGTAGACGTTTC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 26 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAAGGGAAATTTAAAAAAGGGGGGCCCGGGAAAGGG', 'seq': 'ACTCAAACACTCCCAGAGGACGGCACTCTGCATGGGACGCCATCCAGCTCCTTTGACTGTGGAATCAAGTACATTATCAGCTGGCCCCTGGCTCCTGGCT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 27 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCGGGTTTGGGTTTAAACCCTTTTTTTTTAAACCC', 'seq': 'ACAAGTATAATTTTGATACAATGATATATGTGACAGATAAAGGACAAAAAAAGCATTTTCAGCAAGTATTCCAAATGCTGAAGATCATGGGATATGACTG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 28 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGGGGCCCGGGAAACCCGGGGGGCCCAAATTTTTT', 'seq': 'GCTGGAGTGCAGTGGAGCAATCTCGGCTCATTGAACCTCTTGGGTTCAAGTGATTCTTGTGCCTCAGCCTCCCAAGTAGCTGGAATTACAGGCACATACC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 29 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCAAATTTAAACCCCCCCCCGGGGGGTTTTTTGGG', 'seq': 'CAAGATCCTGCCCGGCCTGTACATCGGCAACTTCAAAGATGCCAGAGACGCGGAACAATTGAGCAAGAACAAGGACAAGACATTTCAAAGAAAGTATTAA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 30 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTCCCCCCAAACCCTTTGGGGGGGGGAAAGGGTTT', 'seq': 'ACAGCCGGGCGCCCGTCGGGCTCTGGGAGAGAGCGAGAGAGAAATCCGGTTAAAATCAGAGTCGGAGGGAGGTTTAACCACAGATCGGTTCCGATCGGAT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 31 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTCCCCCCGGGCCCTTTAAATTTGGGGGGTTTGGG', 'seq': 'TTGCCCTCTGACTTGCAGATGCTGTGAGATCCAGAGCTAAGACTCCACGACATCCCGGAAGCCGAAAAATGAATCAGTCTCAGTGTTTCCTGTTTGGATT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 32 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGAAAAAAGGGGGGCCCTTTTTTAAAAAACCCCCC', 'seq': 'GCAGGGAACTGAGGCCGCCTGCCCACATCCATGTGAGTGACCGTCTGGAAGCAGACCTCCAGCCCCAGTCCCGCCTCTGGAGGACTGCAGCCTGCACCTG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 33 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTGGGCCCGGGTTTTTTAAATTTGGGGGGCCCGGG', 'seq': 'GTTATTATTTTAAAAATTAGCTAACTTCTCTCACGGTGTCCTCCCAATATGCACCTTTTGCTCCTAGTGTCCAGATACCTAGCTTTGTATCATTATTTTT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 34 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGTTTAAATTTTTTTTTTTTGGGTTTCCCGGGCCC', 'seq': 'GCTGCCTGCTGATCCGCGCCTAGAGTTTGACCAGCCACTCTCCAGCTCGGCTTTCGCGGCGCCGAGATGCTGTCCTGCCGCCTCCAGTGCGCGCTGGCTG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 35 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGCCCAAATTTAAAGGGCCCAAACCCCCCAAATTT', 'seq': 'CGCGCCCGGCCAAATAAAATAAAATGTTAAAGCAAATTCAGGACTACCCCTCCTCCAAGTCTTCTGTTCCCTTTGGGCGCCCAGGTGAGCGGGGGAGGGG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 36 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAAGGGAAACCCAAAAAATTTAAACCCAAATTTGGG', 'seq': 'TTTGGCTGTCCGGACGGTGCAGCGGCGAGGCCGGCCGCGAAGATGCCAGTGGCGGTGATGGCGGAAAGCGCCTTTAGTTTCAAAAAGTTGCTGGATCAGT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 37 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCTTTCCCTTTGGGTTTGGGTTTCCCGGGAAACCC', 'seq': 'CTGTGCAGCTGCTGCTCGTGGCAGCCTGGAGCATGGGCTGTGGTGAGGCCCTCAAGTGCTACACCTGCAAGGAGCCCATGACCAGTGCTTCCTGCAGGAC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 38 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGTTTAAAGGGAAAGGGTTTGGGAAAGGGAAATTT', 'seq': 'CGGCCCTGACCGCCCCGTGTCCGGCCAGGATCAACTCGTAGGCTTTACGAGAAGAAGATCTTCGAGTACGAGACCCAGAGGCGGCGGCTCTCGCCCCCCA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 39 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTGGGGGGAAAGGGAAAAAACCCGGGGGGGGGCCC', 'seq': 'GGCCCCCTGCCTTGAGGAGCAGCCTTTTTGCTTTCTTTCTTTGGGATAGGATGCCTCTGGGGTTCTTTCTCCCGCAGCCGGCTGTGTTTTAGAGCACTTT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 40 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAAGGGTTTAAACCCAAAGGGTTTGGGGGGAAAAAA', 'seq': 'ACTTAGAACAGCTGGCATCTAACAAAGACTAGCTGTGTCAGCGTGTTATGATGCCGTCCCGTACCAACCTGGCTACTGGAATCCCCAGTAGTAAAGTGAA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': False}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 41 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGTTTCCCCCCGGGGGGCCCTTTAAAAAAAAATTT', 'seq': 'TCCCTTCTGGGTGTTATGGAAGAGTGGCTCCACGGTCAGGCTTGGCTGCAAAACACTTTATTGATGTAGGAGGGCTTTTGTTTGGGGTAGAGTATTAATA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 42 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGCCCGGGGGGAAACCCAAATTTGGGTTTGGGAAA', 'seq': 'TGCAGTTCTGTGAGAGGAAACAACAGCTAACCGGAGCCAGAATTTATACATATTTGCTAGAGAAATCCAGACTTGTTTCACAACCTCTTGGCCAGAGCAA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 43 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAAAAACCCGGGTTTAAAAAAAAAGGGGGGAAAAAA', 'seq': 'CCCCTCTCCCAGGAGACTGGTCTCTGTGCTGACTTCCACCCGAGTGGGGCAGTTGTGGCCGTAGGACTGAACACGGGGAGGTGGTTGGTTTTGGACACAG', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 44 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGAAATTTGGGAAATTTAAACCCAAACCCCCCCCC', 'seq': 'CATGCGACCCCCTTTCACCTACGCCACGCTCATCCGCTGGGCCATCCTGGAGGCTCCAGAGAAGCAGCGGACACTCAATGAGATCTACCACTGGTTCACA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 45 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCGGGGGGAAAAAACCCTTTCCCGGGCCCTTTAAA', 'seq': 'TCCGCCCTGGCACTTCAGAAACGCTGAAACGTTTCATGGCAGAGCAGCTGAACCAGGAGCAGCAGCAGATTCCTGGAAAACCAGGCACTTTCACTTGGCA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 46 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'GGGCCCAAACCCTTTTTTCCCGGGAAACCCCCCGGG', 'seq': 'CTCAAGTGCCTCATCGTGGCCCTGCCCAAGATCATCCTGGCTGTCAAGTCCAAGGGAAAGTTCTATCTGGTCATCGAGGAGCTGAGCCAGCTGTTCCGAT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 47 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'AAAAAATTTGGGCCCAAAAAACCCAAACCCGGGAAA', 'seq': 'TGCAAGAATGCCGATGGAGTGGAGTTGTACAATGAGATTGAGTTCTATGCCAAAGTGAACTCCAAGGACTCCCAGGATAAGCGCTCTTCCCGCTCTATTA', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 48 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCGGGCCCTTTTTTAAAGGGCCCAAACCCAAAAAA', 'seq': 'TTTTAGTCTGTGAACTATAATATTCATGAGACGCTTAACACTTCCCAAAGTGGCAGGGAGGAAACTCTTTGTTTCTTCTGATTCCACCGGAAGAGAGAGT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 49 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'CCCAAAAAAGGGCCCAAAGGGCCCTTTGGGGGGCCC', 'seq': 'GGTTACTGTGGGCAGCTTGAAGACCTCAGCGGTGCCCAGTACCTCCACGATGTCCCAAGAGCCTGAGCTCCTCATCAGTGGAATGGAAAAGCCCCTCCCT', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
17/07/2024 14:04:21 logger: ======>Read 50 generation
17/07/2024 14:04:21 logger: =========>UMI generation start
17/07/2024 14:04:21 logger: ============>UMI condition 0: umi
17/07/2024 14:04:21 logger: =========>Sequence generation start
17/07/2024 14:04:21 logger: ============>Sequence condition 0: seq
17/07/2024 14:04:21 logger: ============>Custom-designed condition 0: custom
17/07/2024 14:04:21 logger: ============>Custom-designed condition 1: custom_1
{'umi': 'TTTTTTAAATTTAAAAAAGGGAAAGGGGGGGGGCCC', 'seq': 'ACATTGGCAGCTGTGCCCGGAGAGGCCTCCAGGGTCCAGCAGAGAAAGGAGTCGAAGAAGCCACCAGCCAAGCTGCAGCCCCGAGCTCTAGCAGGCTGGC', 'custom': 'AAGC', 'custom_1': 'V'}
{'read_mut': {'mark': False}, 'read_del': {'mark': True}, 'read_ins': {'mark': False}}
0
0
0
17/07/2024 14:04:21 logger: ===>Time for sequencing library preparation: 6.757s

Process finished with exit code 0

Understanding files

The resultant files of the simulated sequencing library are shown in the following picture.

Image title
Fig 1. Generated files of a sequencing library

In this case, we used homotrimer blocks to simulate UMIs where the length of each UMI is set to be 36 containing 12 trimer blocks.

Image title
Fig 2. Simulated UMIs

The sequences are randomly chosen from the input human cDNAs and truncated according to the length of each short read.

Image title
Fig 3. Simulated genomics sequences

The sequencing library is tabulated to a dataframe. Each row shows the necessary information about the read 1

  1. Sequence
  2. Identifier
  3. Source

Init means a read 1 is a sequence from the sequencing library, to differ from those from PCR amplification.

Image title
Fig 4. Simulated sequencing library

We set a big integer as an initial seed to sequentially simulate each UMI sequence. Then, users can use the saved seeds to reproduce the experiment.

Image title
Fig 5. Seeds for simulating UMIs

The chosen gene symbols are recorded, each corresponding to the source of the truncated sequence by order.

Image title
Fig 6. Seeds for simulating cDNAs