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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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