pIRS is a profile-based Illumina paired-end Reads Simulator. It can simulate reads from haploid or diploid genomes using precomputed profiles from real data. Alternatively users can generate their own profiles.

References:

• X. Hu et al. pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics 28, 1533-1535 (2012). PubMed |  Journal

• pirs on GitHub

• Module Name: pirs (see the modules page for more information)
• Read simulation is multithreaded. Please match the number of threads to the number of allocated CPUs
• Example files in $PIRS_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=6g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load pirs
[user@cn3144]$ cp $PIRS_TEST_DATA/chr22.fa .

Haplotype data can be simulated directly using the built in profile.

[user@cn3144]$ pirs simulate -l 100 -x 10 -m 200 -z -S 139347 \
                   --threads=$SLURM_CPUS_PER_TASK -o haplo_reads chr22.fa
[pIRS] Program:        pirs (Profile-based Illumina pair-end Reads Simulator)
[pIRS] Version:        2.0.0
[pIRS] Author:         Jianying Yuan (BGI-Shenzhen)
[pIRS] Contact:        yuanjianying@genomics.org.cn
[pIRS] Compile Date:   Oct 25 2019 time: 14:47:51
[pIRS] Current time:   Fri Oct 25 17:56:04 2019
[pIRS] Command line:   pirs simulate -l 100 -x 10 -m 200 -z -S 139347 --threads=4 -o haplo_reads chr22.fa
[pIRS]
[pIRS] Loading base-calling profile /usr/local/apps/pirs/2.0.2/share/pirs/Base-Calling_Profiles/humNew.PE100.matrix.gz
...

To get reads for a simulated diploid genome, first generate a second haplotype then simulate reads for both of them together.

[user@cn3144]$ pirs diploid -s 0.001 -R 2 -d 0.00001 -v 0.000001 \
                  -o chr22 chr22.fa
[user@cn3144]$ ls -lh chr22*
-rw-r--r-- 1 user staff  50M Oct 25 18:01 chr22.snp.indel.inversion.fa
-rw-r--r-- 1 user staff  50M Oct 25 17:42 chr22.fa
-rw-r--r-- 1 user staff  24K Oct 25 18:01 chr22.indel.lst
-rw-r--r-- 1 user staff 1.4K Oct 25 18:01 chr22.inversion.lst
-rw-r--r-- 1 user staff  50M Oct 25 18:01 chr22.snp.indel.inversion.fa
-rw-r--r-- 1 user staff 951K Oct 25 18:01 chr22.snp.lst

[user@cn3144]$ pirs simulate --diploid -l 100 -x 10 -m 800 -z -S 139347 \
                   --threads=$SLURM_CPUS_PER_TASK -o diplo_reads \
                  chr22.fa chr22.snp.indel.inversion.fa

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. pirs.sh), which uses the input file 'pirs.in'. For example:

#!/bin/bash
module load pirs/2.0.2
pirs simulate -l 100 -x 10 -m 200 -z -S 139347 \
    --threads=$SLURM_CPUS_PER_TASK -o haplo_reads chr22.fa

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=8g pirs.sh

Create a swarmfile (e.g. pirs.swarm). For example:

pirs simulate -l 100 -x 10 -m 200 -z --threads=$SLURM_CPUS_PER_TASK -o haplo_reads_chr1 chr1.fa
pirs simulate -l 100 -x 10 -m 200 -z --threads=$SLURM_CPUS_PER_TASK -o haplo_reads_chr2 chr2.fa
pirs simulate -l 100 -x 10 -m 200 -z --threads=$SLURM_CPUS_PER_TASK -o haplo_reads_chr3 chr3.fa

Submit this job using the swarm command.

swarm -f pirs.swarm -g 8 -t 6 --module pirs