SeqGene | Tool name | SeqGene |
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| URL | http://sourceforge.net/apps/mediawiki/seqgene/index.php?title=SeqGene |
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| Important features | 1. It is an open source software mainly used for quality control, SNP annotation and indel identification, RNA Seq expression analysis, allele specific expression, genotype analysis and pathway analysis.
2. It takes aligned SAM reads as input.
3. It can perform differential expression from the RNA seq data. |
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| Citations | Deng X. SeqGene: a comprehensive software solution for mining exome- and
transcriptome- sequencing data. BMC Bioinformatics. 2011 Jun 29;12:267. PubMed PMID: 21714929; PubMed Central PMCID: PMC3148209. |
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| Year of publication | 2011 |
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| Rank by usage frequency | 100 |
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| Comments | Requires installation of R 2.10 or above (optional for differential expression analysis),
Bioconductor packages such as hash, graph, RBGL, KEGGgraph, Rgraphviz, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db (optional for pathway analysis in RNA-Seq) in the path. |
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| Function | SNP discovery, Indel discovery, Copy number estimation, RNA seq analysis, Software package |
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| Category | Free, Downloadable |
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| License | |
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| Status | Working |
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| Input file format | SAM |
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| Output file format | .rpkm, .qc, WIG, .snpa, .geno, .pheno, .design, .deg, .glist, ,path
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| Operating system | Windows XP 32 bit, 64 bit and Linux X86. |
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| Operating language | Python 2.6 or later |
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| Platform | All available platform |
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| Downloadable file format | |
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