NgsCcts

Shared CCTS NGS apps

This page documents apps installed by the CCTS BMI group in cheaha:/share/apps/ngs-ccts

Links to latest versions of each package are in /share/apps/ngs-ccts/latest.

See also PublicDatasetsNgs for genomes, indices and databases

Microbiome

• QIIME 1.5

Alignment Visualization

• IGV
  • IGV 2.1.23
• igvtools
  • IGVtools 2.1.7

Short Read Aligners

• bowtie
  • bowtie-0.12.7 (linked from Galaxy)
• bowtie2
  • bowtie2-2.0.0-beta7 (download binary)
• bwa
  • bwa-0.6.2 (download src) [NgsCctsBuildBwa]

Short Read (denovo) Assemblers

• velvet
  • velvet_1.2.08 (download src)(NgsCctsBuildVelvet)
• ABySS
  • abyss_1.3.4 (download src)(NgsCctsBuildAbyss)