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)
• Tips for working with TACC resources
• General purpose tools
• Microarray data analysis tools
• Mappers / Aligners
• Gene prediction tools
• SNP discovery
• Splice Junction discovery
• Genome Alignment and Visualization
• De novo genome assembly
• 454 Analysis tools
• Useful scripts
• Software users group meetings
• ZOHO Information

References (by organism)

• Human
• KSHV
• Arabidopsis
• Bacteriophage T7
• Xenopus tropicalis
• Zebrafish (Danio rerio)

General purpose tools

• Blast
• Bioconductor
• Bioperl
• R
• Python Library
• Graphics programs
• BOOST libraries
• ?Phred, Phrap, Consed, cross_match, daev
• Hmmer

Microarray data analysis tools

• MeV

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

• GeneWise
• Geneid

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
• ABYSS

• \[\]

• ABI's SOLiD de novo pipeline
• Allpaths-LG
• (Newbler, the Roche/454 assembler, is under 454 Analysis tools)

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