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Many of these are available via the TACC module system (use module keyword or module spider to search).
The current listing of modules and versions available on Lonestar is also posted here.
In addition, the BioITeam maintains executables in /corral-repl/utexas/BioITeam/bin; we advise adding this directory to your path.
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General purpose tools
Microarray data analysis tools
NGS Data Quality Control Tools
Mappers/Aligners
- mapreads SOLiD data only, ungapped alignment
- MAQ - best for short-read SNP calling; ungapped alignment
- muscle - "old school" aligner - good for 454 amplicons
- SOAP - very fast and versatile: any read length, gapped, paired-end, SNP calling
- SSAHA & SSAHA2 - like Maq, fast for ungapped mapping - SNP calling, contig placement to reference, etc.
- Bowtie - very fast, ungapped alignment. Does not support color space data
- SHRiMP - A sensitive and accurate mapper. Supports color space data and gapped alignment.
- BFAST - BLAT-like short read mapper. Natively supports SOLiD colorspace short reads.
- BWA - The successor to MAQ; a BW mapper, but which allows for gaps and handles colorspace natively.
- GMAP and GSNAP - Mappers for cDNA and very sensitive detection of short indels.
- Mosaik - A suite of alignment and reference-guided assembly tools.
- See Category:Mapper for more details.
Gene prediction tools
SNP discovery and Annotation
RNA-Seq Analysis
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Splice Junction discovery
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Genome Alignment and Visualization
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De novo assembly
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Transcriptome de novo assembly
ABI pipelines
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