Subread carries out high-performance read alignment, quantification and mutation discovery. It is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and DNA-seq reads. It uses a new mapping paradigm called seed-and-vote to achieve fast, accurate and scalable read mapping. Subread automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports INDEL detection and can map reads with both fixed and variable lengths.

For more information, please check its website: and its home page:


  • 1.6.4

  • 2.0.1


  • detectionCall

  • exactSNP

  • featureCounts

  • flattenGTF

  • genRandomReads

  • propmapped

  • qualityScores

  • removeDup

  • repair

  • subindel

  • subjunc

  • sublong

  • subread-align

  • subread-buildindex

  • subread-fullscan

  • txUnique


You can load the modules by:

module load biocontainers
module load subread

Example job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Subread on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 4
#SBATCH --job-name=subread
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers subread

featureCounts -s 2 -p -Q 10 -T 4 -a genome.gtf -o featurecounts.txt mapped.bam