[BioC] Rsubread aligner NEWS

[Wei Shi]

Dear All,

Although our Subread read aligner and Subjunc junction detector have been around for a while, we have just got them published on Nucleic Acids Research today. 

Subread and Subjunc employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. It takes Subread less than 20 minutes to map 10 million 100bp reads using one thread. Its running time remains nearly the same when mapping longer reads thanks to the high scalability of the seed-and-vote paradigm.

Subread and Subjunc can be used to map reads generated from all major sequencing platforms including Illumina GA/HiSeq, Roche 454, ABI SOLiD and Ion Torrent.

The Rsubread package provides access functions, called 'align' and 'subjunc', respectively, for Subread and Subjunc. This package also includes other useful functions such as quality assessment ('qualityScores'), read summarization ('featureCounts') and absolute expression calling ('detectionCall'), providing an integrated toolkit for processing gDNA and RNA sequencing data.

The Rsubread package in the latest Bioc release (2.12) can be run on both Linux/unix and Mac computers.

Our paper for Subread and Subjunc can be freely accessed at: http://nar.oxfordjournals.org/content/early/2013/04/03/nar.gkt214.abstract 

Hope you found them useful.


Best regards,
------------------------
Wei Shi, Ph.D
Bioinformatics Division,
The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville 3052, Victoria
Australia

 

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