Software
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The following is a categorized list of software available through the GSAF. Each page lists a summary of the software, the hardware it is currently installed on, links to user documentation, and helpful tips.
Contents
References (by organism)
Galaxy Workflows
General purpose tools
Microarray data analysis tools
Mappers/Aligners
- mapreads SOLiD data only, ungapped alignment
- MAQ - best for short-read SNP calling; ungapped alignment
- 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.
- See Category:Mapper for more details.
Gene prediction tools
SNP discovery
- Corona-Lite - SOLiD data only
- MAQ - best for short-read SNP calling; ungapped alignment
- SOAP - very versatile: any read length, gapped, paired-end, SNP calling
- SAMTOOLS
Splice Junction discovery
Genome Alignment and Visualization
- IGV
- MaqView
- Mauve
- Affymetrix Integrated Genome Browser: easy to install genome browser. Download here
De novo assembly
ABI pipelines
454 Analysis tools
Useful scripts
Software users group meetings
- Small-rna data analysis - Lessons learned during Sullivan data analysis
- Mapping of short reads - Comparison of few publicly available mapping tools