IsoSeqSim is an Iso-Seq reads simulator for evaluating the performance of Iso-Seq bioinformatics analysis tools

Web site

• Home page

• Module Name: isoseqsim (see the modules page for more information)
• Executable Name: isoseqsim

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
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 isoseqsim
[+] Loading isoseqsim  0.2  on cn3144 
[+] Loading singularity  4.2.2  on cn3144 

[user@cn3144 ~]$ isoseqsim -h
usage: isoseqsim [-h] [-v] [-m {normal,fusion,apa,ase,ats}] -g GENOME -a
                 ANNOTATION -o OUTPUT -t TRANSCRIPT --tempdir TEMPDIR
                 [--nbn NBN] [--nbp NBP] [--cpu CPU] --c5 C5 --c3 C3 [--es ES]
                 [--ei EI] [--ed ED] [--fc FC] [--dis_pa DIS_PA]
                 [--dis_tss DIS_TSS] [--vcf VCF] [--id ID] [--tnl TNL]
                 [--tnu TNU] [--tnm TNM] [--tns TNS]
isoseqsim: error: argument -g/--genome is required
[...]

[user@cn3144 ~]$ cd /data/$USER
[user@cn3144 ~]$ git clone https://github.com/yunhaowang/IsoSeqSim.git
[user@cn3144 ~]$ cd IsoSeqSim
[user@cn3144 ~]$ isoseqsim -g example/input/genome.fasta -a example/input/gene_annotation.gtf --c5 utilities/5_end_completeness.PacBio-P6-C4.tab --c3 utilities/3_end_completeness.PacBio-P6-C4.tab -o example/simulated_reads_normal.fa -t example/simulated_transcipt_normal.gpd --tempdir example/temp_normal
### Start analysis at Mon,05 May 2025 13:30:02
## Mode: normal
# Step1: convert gtf to gpd
Start analysis: Mon,05 May 2025 13:30:02
Finish analysis: Mon,05 May 2025 13:30:02
# Step2: generate transcriptome fasta file
Start analysis: Mon,05 May 2025 13:30:03
Finish analysis: Mon,05 May 2025 13:30:03
# Step3: generate expression matrix based on Negative Binomial distribution
Start analysis: Mon,05 May 2025 13:30:03
Finish analysis: Mon,05 May 2025 13:30:03
# Step4: simulate Iso-Seq reads
Start analysis: Mon,05 May 2025 13:30:03
Finish analysis: Mon,05 May 2025 13:30:15
### Finish analysis at Mon,05 May 2025 13:30:15

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

Create a batch input file (e.g. isoseqsim.sh). For example:

#!/bin/bash

module load isoseqsim

cd /data/$USER/IsoSeqSim

isoseqsim -g example/input/genome.fasta \
          -a example/input/gene_annotation.gtf \
          --c5 utilities/5_end_completeness.PacBio-P6-C4.tab \
          --c3 utilities/3_end_completeness.PacBio-P6-C4.tab \
          -o example/simulated_reads_normal.fa \
          -t example/simulated_transcipt_normal.gpd \
          --tempdir example/temp_normal

Submit this job using the Slurm sbatch command.

sbatch [--gres=lscratch:#] [--cpus-per-task=#] [--mem=#] isoseqsim.sh

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

cd /data/$USER/IsoSeqSim1; \
isoseqsim -g input/genome.fasta \
          -a input/gene_annotation.gtf \
          --c5 utilities/5_end_completeness.PacBio-P6-C4.tab \
          --c3 utilities/3_end_completeness.PacBio-P6-C4.tab \
          -o simulated_reads_normal.fa \
          -t simulated_transcipt_normal.gpd \
          --tempdir /lscratch/$SLURM_JOB_ID/temp1
cd /data/$USER/IsoSeqSim2; \
isoseqsim -g input/genome.fasta \
          -a input/gene_annotation.gtf \
          --c5 utilities/5_end_completeness.PacBio-P6-C4.tab \
          --c3 utilities/3_end_completeness.PacBio-P6-C4.tab \
          -o simulated_reads_normal.fa \
          -t simulated_transcipt_normal.gpd \
          --tempdir /lscratch/$SLURM_JOB_ID/temp2
cd /data/$USER/IsoSeqSim3; \
isoseqsim -g input/genome.fasta \
          -a input/gene_annotation.gtf \
          --c5 utilities/5_end_completeness.PacBio-P6-C4.tab \
          --c3 utilities/3_end_completeness.PacBio-P6-C4.tab \
          -o simulated_reads_normal.fa \
          -t simulated_transcipt_normal.gpd \
          --tempdir /lscratch/$SLURM_JOB_ID/temp3

Submit this job using the swarm command.

swarm -f isoseqsim.swarm [--gres=lscratch:#] [-g #] [-t #] --module isoseqsim