Subread protocols

Subread computational protocol

Subread specifications


Unique identifier OMICS_01255
Name Subread
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.6.2
Stability Stable
Maintained Yes


  • exactSNP
  • featureCounts
  • Subindel
  • Subjunc
  • Sublong



Add your version



  • person_outline Wei Shi <>

Publications for Subread

Subread IN pipelines

PMCID: 5852578
PMID: 29439397
DOI: 10.3390/genes9020082

[…] 10 fastq files for 0–2 h and 11 fastq files for 6–8 h embryonic transcripts from modencode [44]. all fastq files were aligned to drosophila melanogaster genome (dmel-r6.18) using gsnap [45]. featurecounts [46,47] was used to assign reads to each gene using gtf file (dmel-all-r6.18.gtf) downloaded from we used r package deseq2 [48] to normalize reads, calculate fold changes […]

PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] the parasponia reference genome with hisat2 version 2.02 (103) using an index that includes exon and splice site information in the rna-seq alignments. mapped reads were assigned to transcripts with featurecounts version 1.5.0 (104). normalization and differential gene expression were performed with deseq2. nodule enhanced genes were selected based on >2.0-fold change and p ≤ 0.05 […]

PMCID: 5207713
PMID: 28045981
DOI: 10.1371/journal.pone.0169074

[…] alignment reference. the hpv genome sequences were downloaded from the ncbi genbank database. a count of sequence reads that mapped to each reference genome were calculated by featurecount from the subread package v1.4.6 [31]. alignments and counting were run on 12 parallel search threads. to identify as many true positives as possible and at the same time keep false positives at a minimum, […]

PMCID: 5327466
PMID: 28240248
DOI: 10.1038/srep43495

[…] reads were right-trimmed for the illumina adapter sequence using flexbar ( and aligned with bowtie219. counting reads over annotated features was done with featurecounts20. annotation was taken from tuberculist release r27. to avoid the influence of transcripts deriving from the original 5′ fragment of mmpl3, a truncated version of mmpl3 was added […]

PMCID: 5385341
PMID: 28443133
DOI: 10.3389/fgene.2017.00041

[…] each fragment to allow a more direct comparison with the single-ended data. reads were mapped to the mouse genome (grcm38) using hisat2 (kim et al., 2015) and annotated transcripts quantified with featurecounts (liao et al., 2014). differential expression analysis was performed using deseq2 (love et al., 2014). alpha cell, beta cell, and islet data were then subjected to pairwise comparisons […]

Subread institution(s)
Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, Australia; Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
Subread funding source(s)
Supported by the Project Grant [1023454] and a Fellowship from the Australian National Health and Medical Research Council (NHMRC); Victorian State Government Operational Infrastructure Support; Australian Government [NHMRC IRIIS].

Subread reviews

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Arup Ghosh

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Very fast and easy to use tool for extracting raw read counts from aligned files. This tool can take multiple aligned files together and combines the output in one file for further analysis.


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Easy to use. I routinely use featureCounts for RNA-Seq data it is much faster than HTSeq-count for generating read counts.