200bp) as well." /> Bioconductor - Rsubread

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rsubread")

In most cases, you don't need to download the package archive at all.

Rsubread

   

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads

Bioconductor version: 2.8

This package provides an R interface to the Subread aligner (http://sourceforge.net/projects/subread/) for mapping next-gen sequencing reads. Subread aligns reads to the referenc genome by using a set of substrings(subreads) extracted from each read. The consensus location mapped by subreads directly determines the mapping location of the read. Therefore, there is no costly extension step as in the "seed-and-extend" mapping paradig. Subread achieves much higher mapping speed and mapping sensitivity than "seed-and-extend" aligners at no cost to the accuracy. Subread aligner can align reads from all the major platforms inculding Illumina GA/HiSeq, ABI SOLiD, Roche 454 and HeliScope. It supports the mapping of paired-end reads and it also allows a large number of indels in the mapping. It can be used to align long reads (>200bp) as well.

Author: Wei Shi, Yang Liao and Jenny Zhiyin Dai

Maintainer: Wei Shi <shi at wehi.edu.au>

Citation (from within R, enter citation("Rsubread")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rsubread")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Rsubread")

 

PDF Rsubread.pdf
PDF   Reference Manual

Details

biocViews HighThroughputSequencing, Sequencing, Software
Version 1.1.1
In Bioconductor since BioC 2.8 (R-2.13) (5 years)
License LGPL-3
Depends
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL http://bioconductor.org/packages/release/bioc/html/Rsubread.html
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source Rsubread_1.1.1.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Rsubread/tree/release-2.8
Package Short Url http://bioconductor.org/packages/Rsubread/
Package Downloads Report Download Stats

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