ShortRead pipeline

ShortRead specifications


Unique identifier OMICS_01076
Name ShortRead
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Martin Morgan <>

Publication for ShortRead

ShortRead IN pipelines

PMCID: 5888676
PMID: 29394375
DOI: 10.1093/nar/gky058

[…] the reference genome hg19 using bowtie (33). peak calling was performed using macs (34). the detected peaks were annotated using snpeff (35). for rna-seq data, the quality control was performed with shortread package (36) in r/bioconductor ( (37). low quality (score < 20) bases were trimmed from both ends of the reads. trimmed reads shorter than 40nt or containing […]

PMCID: 5293829
PMID: 28223970
DOI: 10.3389/fmicb.2017.00156

[…] using the bandage graph visualization (wick et al., 2015) software and its integrated blast tool. querying of short sequences against the raw sequence reads in fastq format was performed using the r shortread (morgan et al., 2009) package., the raw genome data generated for this study are deposited in the sra database: accession no. srp096281., we used the parsnp rapid genome alignment tool, […]

PMCID: 4852503
PMID: 26822477
DOI: 10.1242/dmm.022905

[…] following generation of sequence, reads were aligned to the mouse genome version ncbi m37 using tophat ( quality control of sequencing data was accomplished by using the shortread package in r ( aligned reads were mapped to ensembl transcript models and converted to reads per kilobase of transcript per million mapped reads (rpkm) values […]

PMCID: 5118689
PMID: 27874090
DOI: 10.1038/srep37563

[…] is used only once., the linkage of barcodes to genomic fragments and the consecutive calculation of the purity parameter was conducted inside the r statistical package18 (fig. 3) with bioconductor shortread package with critical components implemented from stand-alone software projects such as bbmap19, starcode15 and bowtie220 (see materials and methods for details or the full git repository […]

PMCID: 4165759
PMID: 25226037
DOI: 10.1371/journal.pbio.1001950

[…] core facility, university of california, riverside, for single-end sequencing with 100 cycles using the illumina hiseq2000 platform. raw data in fastq file format were imported into r using the shortread package [46], the barcode sequence was removed from the 100 bp read sequences and reads were aligned to the a. thaliana genome tair10 version ( using bowtie (ver. […]

ShortRead institution(s)
Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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