Simply generates subsequences of a specified length from a supplied reference sequence, applying base insertions, deletions and substitutions at specified rates
Simulates:
- Sequencing of a randomly mutated reference genome
- Single reads of a defined length
- Substitutions, insertions and deletions at specified rates
- Insertions and deletions of geometrically distributed length (default p=0.25)
- Insertions of random composition
- Insertions and deletions of geometrically distributed length (default p=0.25)
- Forward and reverse complement reads
Does not simulate:
- Read quality
- Realistic sequencing error profiles
- CIGAR values
- Python3
- Argh (
pip install argh) - NumPy (
pip install numpy) - Biopython (
pip install biopython)
$ ./sod.py -h
usage: sod.py [-h] [-n N_READS] [-r READ_LEN] [-s SUB_RATE]
[--ins-rate INS_RATE] [-d DEL_RATE]
[--indel-ext-rate INDEL_EXT_RATE] [-f] [-u]
path-to-ref
Command line interface
positional arguments:
path-to-ref -
optional arguments:
-h, --help show this help message and exit
-n N_READS, --n-reads N_READS
1
-r READ_LEN, --read-len READ_LEN
150
-s SUB_RATE, --sub-rate SUB_RATE
0.0
--ins-rate INS_RATE 0.0
-d DEL_RATE, --del-rate DEL_RATE
0.0
--indel-ext-rate INDEL_EXT_RATE
0.25
-f, --fastq False
-u, --uppercase False
$ ./sod.py -n 1 --read-len 150 --sub-rate 0.05 --ins-rate 0.05 --del-rate 0.05 tests/hxb2.fasta
>read1_r8456_s8_i9_d4
TCTGTCTCTGTCTCaCTCTCgCACgtCtTTCTTCctCTATTCCTTCGGcGCCTGTCGGGT
CcgGcGgGTTGAGGTGGGTCTGAAACGATAATGGTGAATATCaCcCTGCaCTAACaCTAT
TCACTATAAAAGTACAGCaAAAACTAaTTC