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

• [ tophat]
  • tophat-2.0.6 (binary)
• bowtie
  • bowtie-0.12.7 (linked from Galaxy)
  • bowtie-0.12.8 (binary)
• 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)
    • MAXKMERLENGTH = 57
    • LONGSEQUENCES

in process

• ABySS NOT DONE
  • abyss_1.3.4 (download src)(NgsCctsBuildAbyss)
    • maxk=100
• VICUNA from Broad Institute - Viral genome denovo assembler NOT DONE
  • VICUNA_v1.2 [1]
  • V-FAT [2]
  • V-Phaser & V-Profiler [3]