You do not have permission to edit this page, for the following reason:
The action you have requested is limited to users in the group: Users.
Short description:
Please summarise the application in a few sentences. Avoid links here. Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called "seed-and-vote" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Next Generation Sequencing, RNA-Seq alignment, Mapping, Whole genome resequencing,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Read mapping,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina, ABI SOLiD, Ion Torrent, 454,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Australia The Walter and Eliza Hall Institute,
Subjunc is a specialized RNA-seq read aligner that can detect exon-exon junctions in addition to the read alignment. Subjunc reports full alignment for every read including exon-spanning reads. Subjunc should be used if the purpose of the analysis is to find exon-exon junctions or to discover genomic variations (eg. SNPs) in the RNA-seq data. Both Subjunc and Subread can be used for mapping if the purpose of RNA-seq analysis is to perform an expression analysis (eg. finding differentially expressed genes), however Subread is recommended because it is faster. Running time of Subread and Subjunc is mainly determined by the number of subreads/seeds used for mapping, not by the read length. Therefore they have a very good scalability with the read length. 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 described in the following paper: Liao Y, Smyth GK and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013
Once you save the form, you will have the chance to add links and references.
Summary of edit
This is a minor edit Watch this page
Cancel