Difference between revisions of "Subjunc"
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|sw summary=The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-exon junctions from RNA-seq data. 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. They can run on both Linux/unix and Mac computers. Subread and Subjunc were published in Nucleic Acids Research in 2013. | |sw summary=The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-exon junctions from RNA-seq data. 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. They can run on both Linux/unix and Mac computers. Subread and Subjunc were published in Nucleic Acids Research in 2013. | ||
|bio domain=Alternative Splicing, Next Generation Sequencing, RNA-Seq Alignment, | |bio domain=Alternative Splicing, Next Generation Sequencing, RNA-Seq Alignment, | ||
− | |bio method=Alternative Splicing, Read | + | |bio method=Alternative Splicing, Read alignment, |
|bio tech=Illumina HiSeq, ABI SOLiD, Ion Torrent, 454, | |bio tech=Illumina HiSeq, ABI SOLiD, Ion Torrent, 454, | ||
|created by=Wei Shi and Yang Liao, | |created by=Wei Shi and Yang Liao, |
Revision as of 08:32, 24 August 2015
Application data |
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Created by | Wei Shi and Yang Liao |
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Biological application domain(s) | Alternative Splicing, Next Generation Sequencing, RNA-Seq Alignment |
Principal bioinformatics method(s) | Alternative Splicing, Read alignment |
Technology | Illumina HiSeq, ABI SOLiD, Ion Torrent, 454 |
Created at | Australia
The Walter and Eliza Hall Institute |
Maintained? | Yes |
Input format(s) | fastq |
Summary: The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-exon junctions from RNA-seq data. 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. They can run on both Linux/unix and Mac computers. Subread and Subjunc were published in Nucleic Acids Research in 2013.
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