Gene isoform quantification using short and/or long reads.

References:

• Li, H., Wang, D., Gao, Q. et al. Improving gene isoform quantification with miniQuant. Nature Biotechnology. 2025 Jun 03; 44, 477-489.

• miniQuant on GitHub

• Module Name: miniquant (see the modules page for more information)
• Multithreaded using the -t argument.
• Environment variables set
  • MINIQUANT_HOME
• Example files in $MINIQUANT_HOME/example

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 miniquant

[user@cn3144 ~]$ miniQuant quant \
  -r $MINIQUANT_HOME/example/reference.fa \
  -l $MINIQUANT_HOME/example/LR.fasta.gz \
  -t 2 \
  -o miniQuant_LR_alone_res 

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

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

#!/bin/bash
set -e
module load miniquant
miniQuant quant \
  -r $MINIQUANT_HOME/example/reference.fa \
  -l $MINIQUANT_HOME/example/LR.fasta.gz \
  -t ${SLURM_CPUS_PER_TASK:-2} \
  -o miniQuant_LR_alone_res

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] miniquant.sh

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

miniQuant quant -r $MINIQUANT_HOME/example/reference.fa -l LR1.fasta.gz -t ${SLURM_CPUS_PER_TASK:-2} -o sample1
miniQuant quant -r $MINIQUANT_HOME/example/reference.fa -l LR2.fasta.gz -t ${SLURM_CPUS_PER_TASK:-2} -o sample2
miniQuant quant -r $MINIQUANT_HOME/example/reference.fa -l LR3.fasta.gz -t ${SLURM_CPUS_PER_TASK:-2} -o sample3
miniQuant quant -r $MINIQUANT_HOME/example/reference.fa -l LR4.fasta.gz -t ${SLURM_CPUS_PER_TASK:-2} -o sample4

Submit this job using the swarm command.

swarm -f miniquant.swarm [-g #] [-t #] --module miniquant