Software

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="d9ed0321-15e7-4900-952e-33b05a9779b5"><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="4537c6e0-de45-42f1-9803-83ac2287bcbd"><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="560c7b8d-7da7-4ecf-b8e7-dab1968ca978"><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="e53d6578-048b-4616-8c20-af1aa82355ed"><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="904b0d16-ac72-4e60-a564-a61f1ccfc247"><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="1015305b-02d9-4a29-8963-ffa8a4cde810"><ac:parameter ac:name="">align</ac:parameter></ac:structured-macro>
  ----
  * IGV
  * MaqView
  * Mauve
  * Affymetrix Integrated Genome Browser: easy to install genome browser. Download here
  De novo genome assembly<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="2a0f309b-5055-406e-b40c-b020d575998b"><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