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
- 1 References (by organism)
- 2 General purpose tools
- 3 Microarray data analysis tools
- 4 Mappers
- 5 SNP discovery
- 6 Splice Junction discovery
- 7 Genome Alignment and Visualization
- 8 de novo genome assembly
- 9 454 Analysis tools
- 10 Useful scripts
- 11 Software users group meetings
References (by organism) - Human
- KSHV
- Arabidopsis
- Bacteriophage T7
- Xenopus tropicalis
- Zebrafish (Danio rerio)
General purpose tools - Blast
- Bioconductor
- Bioperl
- R
- Python Library
- Graphic programs
Microarray data analysis tools - MeV
Mappers - 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 - 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.
- See Category:Mapper for more details.
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 - Tophat
Genome Alignment and Visualization - MaqView
- Mauve
- Affymetrix Integrated Genome Browser: easy to install genome browser. Download here
De novo genome assembly - MIRA
- Velvet
- ABI's SOLiD de novo pipeline
- Allpaths-LG
454 Analysis tools - Sff file manipulation tools - Utilities to convert and manipulate 454 sff files.
- GS De novo assembler - Performs assembly of reads and generates contigs.
- GS Reference mapper - Maps reads to a reference genome and reports consensus and variants.
- GS Amplicon variant analyzer - For detection of variants in amplicon libraries : a small region of interest at very large coverage.
- GS Run processor and run browser - Generally run already by the GSAF, but you might want to re-process image data sometimes.
- Georgiou Lab Amplicon scripts - Matlab scripts...
- BLAST tools - Scripts for quick and dirty blasts of 454 reads and contigs to see what's going on at a global level
Useful scripts - General parser scripts - scripts for parsing and filtering of fasta, fastq files and output files from different mappers; base space, color space conversion scripts.
- Small rna analysis
- Generation of wig files from mapreads output
- Conversion of mapreads output to GFF, SAM, or BAM format - These utilities can be used to convert mapreads mapping output to base space format
- Generation of gene counts from results of mapping to genome - These scripts can be used to identify the reads that correspond to genes, after mapping to the genome.
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
