Subread
|
Application data |
|
| Created by | Wei Shi and Yang Liao |
|---|---|
| Biological application domain(s) | Next Generation Sequencing, RNA-Seq alignment, Mapping, Whole genome resequencing |
| Principal bioinformatics method(s) | Read mapping |
| Technology | Illumina, ABI SOLiD, Ion Torrent, 454 |
| Created at | Australia
The Walter and Eliza Hall Institute |
| Maintained? | Yes |
| Input format(s) | (C)FAST(A/Q) |
| Output format(s) | SAM |
| Software features | Gapped alignment, Local alignment, Memory efficient and fast, Paired read support, RNAseq analysis, SAM format output, SNP/indel discovery in any format, can run on major computer platforms, capable of using very small seeds for splice mapping, low cost for high-error matching, paired-end mapping, parallel execution, parallel execution, short and long reads |
| Programming language(s) | C |
| Licence | GPLv3 |
| Operating system(s) | Linux 64, Mac OS X, Mac OS X; x86 64 |
Summary: 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.
"Error: no local variable "counter" was set." is not a number.
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
Links
References
To add a reference for Subread, enter the PubMed ID in the field below and click 'Add'.
Search for "Subread" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
