ShortRead protocols

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ShortRead specifications

Information


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
Version 1.16.4
Stability Stable
Requirements
methods, BiocGenerics, Biobase, IRanges, GenomicRanges, Rsamtools, Biostrings, zlibbioc, lattice, RUnit, biomaRt, GenomicFeatures, latticeExtra, BiocGenerics(>=0.1.0), IRanges(>=1.13.4), GenomicRanges(>=1.7.43), Biostrings(>=2.25.6), Rsamtools(>=1.7.42), hwriter, yeastNagalakshmi
Maintained Yes

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Maintainer


  • person_outline Martin Morgan <>

Publication for ShortRead

ShortRead in pipelines

 (30)
2018
PMCID: 5811965
PMID: 29439679
DOI: 10.1186/s12881-018-0528-6

[…] established mody genes and those that were implicated in pancreatic cell biology and/or diabetes (additional file : table s3)., all sequencing reads were evaluated for quality using the bioconductor shortread package []. an all-against-all sample comparison was done on germline variants to confirm the patient exome-wgs data pairing and establish sample relatedness prior to additional data […]

2018
PMCID: 5856545
PMID: 29483267
DOI: 10.1073/pnas.1719455115

[…] facility of weill cornell medical college., the rna-seq analysis protocol was adopted a previously described protocol (). the reads were collected and verified by sequence quality control with shortread. using tophat2 software, the reads were aligned to the reference genome arabidopsis_thaliana.tair10.30.gtf, which was downloaded from plants.ensembl.org/info/website/ftp/index.html. the bam […]

2018
PMCID: 5888676
PMID: 29394375
DOI: 10.1093/nar/gky058

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

2017
PMCID: 5343820
PMID: 28134837
DOI: 10.3390/ijms18020284

[…] mirbase v21 was done using the bowtie aligner []. data were compressed with samtools [] to bam format. mapped reads were counted with r/bioconductor programming environment [] by application of the shortread library []. an error rate of 1 nt per mature mirna sequence was allowed. normalization of data was performed by the two independent procedures deseq2 and the tmm algorithm., two-way […]

2017
PMCID: 5389539
PMID: 28130424
DOI: 10.1093/nar/gkx042

[…] were analyzed as described in ()., pcr-products corresponding to expanded crispr array were subjected to high-throughput sequencing with miseq illumina system. the resulting data were analyzed using shortread () and biostrings () bioconductor packages. sequences located between two crispr repeats were considered as spacers. they were mapped on phage genomes with no mismatches allowed. r scripts […]

ShortRead in publications

 (98)
PMCID: 5856545
PMID: 29483267
DOI: 10.1073/pnas.1719455115

[…] facility of weill cornell medical college., the rna-seq analysis protocol was adopted a previously described protocol (). the reads were collected and verified by sequence quality control with shortread. using tophat2 software, the reads were aligned to the reference genome arabidopsis_thaliana.tair10.30.gtf, which was downloaded from plants.ensembl.org/info/website/ftp/index.html. the bam […]

PMCID: 5812932
PMID: 29269494
DOI: 10.1128/AEM.02200-17

[…] obtained, with a median of 115,072 reads/sample., the protocol for initial processing of reads was adapted from the dada2 workflow by greg gloor (github.com/ggloor/miseq_bin), using the dada2 and shortread packages in r version 3.2.2 (www.r-project.org). read quality was determined by plotting quality profiles for both the forward and reverse reads. trimming of reads was performed to remove […]

PMCID: 5825165
PMID: 29432414
DOI: 10.1371/journal.pgen.1007238

[…] per lane and sequenced by hiseq2500 (illumina) with sr52, a 2-bp extended version of sr50, for higher-quality sequencing. after trimming by quasr, 24-nt long srna-seq reads were extracted by shortread [], and mapped to the rice irgsp1.0 genome using tophat, in which reads having >50 multi-hits on rice genome or any mismatches were cut off (-n 0 -g 50). if 24-nt rnas with >10 fpkm […]

PMCID: 5676899
PMID: 29078319
DOI: 10.1073/pnas.1707938114

[…] using the miseq v3 600c paired-end sequencing kit (illumina). paired-end reads were merged by using pear (). fastq files were read by using r (r core team, 2015; https://www.r-project.org/) with the shortread package and converted to fasta files subsequently submitted to imgt/highv-quest () for annotation., all analyses of annotated vdj-seq data were performed by using r in combination […]

PMCID: 5635119
PMID: 29018260
DOI: 10.1038/s41467-017-00812-0

[…] ribo biotechnology co. ltd (www.ribobio.com). rna-seq data were processed, assembled, and annotated as previously described. briefly, rna-seq reads were examined by a custom r script based on the shortread package to remove low-quality (q value <20) reads, adapters, and barcode sequences. high-quality clean reads were assembled de novo into contigs by trinity with strand-specific option […]

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

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