Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Migrated to Confluence 5.3

...

The following is a categorized list of software available through the UT GSAF and/or TACC's life sciences group. Each page lists a summary of the software, the hardware it is currently installed on, links to user documentation, and helpful tips.

Many of these are available via the TACC module system (use module keyword or module spider to search).

The current listing of modules and versions available on Lonestar is also posted here.

In addition, the BioITeam maintains executables in /corral-repl/utexas/BioITeam/bin; we advise adding this directory to your path.

Contents

...

General purpose tools

Anchor
gen
gen

Microarray data analysis tools

Anchor
micro
micro

NGS Data Quality Control Tools

Anchor
qc
qc

Mappers/Aligners

Anchor
map
map

  • mapreads SOLiD data only, ungapped alignment
  • MAQ - best for short-read SNP calling; ungapped alignment
  • muscle - "old school" aligner - good for 454 amplicons
  • 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.
  • GMAP and GSNAP - Mappers for cDNA and very sensitive detection of short indels.
  • Mosaik - A suite of alignment and reference-guided assembly tools.
  • See Category:Mapper for more details.

Gene prediction tools

Anchor
genepred
genepred

SNP discovery and Annotation

Anchor
SNP
SNP

RNA-Seq Analysis

Anchor
rnaseq
rnaseq

Splice Junction discovery

Anchor
splice
splice

...

Genome Alignment and Visualization

Anchor
align
align

...

De novo assembly

Anchor
denovo
denovo

Transcriptome de novo assembly

Anchor
transdenovo
transdenovo

ABI pipelines

Anchor
analysis
analysis

...


Software users group meetings

Anchor
usergroup
usergroup

...