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

• Getting an account on GSAF server-fourierseq
• Tips for working with TACC resources
• References (by organism)
• 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
• BioMart Perl APIs
• NCBI Eutils
• R
• Python Library
• Graphics programs
• BOOST libraries
• ?Phred, Phrap, Consed, cross_match, daev

• [Hmmer]\\ *Microarray data analysis tools{*}<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="188f37bc-7be9-4f8a-b010-2c8cc50adb8d"><ac:parameter ac:name="">micro</ac:parameter></ac:structured-macro> \---\- \* [MeV]\\ *Mappers/Aligners{*}<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="b8572b28-b10d-4f9b-88d3-e130d0d0f157"><ac:parameter ac:name="">map</ac:parameter></ac:structured-macro> \---\- \* [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{*}<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="48961a9e-dcd1-40ee-b24d-00333b1f0eff"><ac:parameter ac:name="">genepred</ac:parameter></ac:structured-macro> \* [GeneWise] \* [Geneid]\\ *SNP discovery{*}<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="c96d05c5-7be8-445a-9a85-afa76d1b2482"><ac:parameter ac:name="">SNP</ac:parameter></ac:structured-macro> \---\- \* 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{*}<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="ed896b2e-23fb-4a83-a6d2-7c5f8625e351"><ac:parameter ac:name="">splice</ac:parameter></ac:structured-macro> \---\- \* [Tophat]\\ *Genome Alignment and Visualization{*}<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="54f90f51-4101-4e6e-9037-fc9392b2810c"><ac:parameter ac:name="">align</ac:parameter></ac:structured-macro> \---\- \* [IGV] \* [MaqView] \* Mauve \* Affymetrix Integrated Genome Browser: easy to install genome browser. Download [here|http://www.affymetrix.com/partners_programs/programs/developer/tools/download_igb.affx]\\ *De novo genome assembly{*}<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="1fe6b418-a824-4313-aac6-440d7d043df4"><ac:parameter ac:name="">denovo</ac:parameter></ac:structured-macro> \---\- \* [MIRA] \* [Velvet] \* [ABYSS] \* \[\] \* [ABI's SOLiD de novo pipeline] \* Allpaths-LG \* (Newbler, the Roche/454 assembler, is under 454 Analysis tools)

ABI pipelines

• Small RNA Pipeline

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.
• Conversion of gene ID's from one form to another (i.e. NCBI to Ensembl & vice-versa)
• Quick tips on GO analysis
• Median polish to consolidate quantitations

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