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

R-packages

• R-packages

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
• MOSAIK
  • mosaik-1.1.0021 - installed in galaxy
  • mosaik-2.1 exe_dist too old, must build from source (download src) NgsCctsBuildMosaik

Short Read (denovo) Assemblers

• velvet
  • velvet_1.2.08 (download src)(NgsCctsBuildVelvet)
    • MAXKMERLENGTH = 57
    • LONGSEQUENCES

SNP analysis

• SnpEff
  • snpeff_3_1 (zip)
    • scripted install of galaxy wrappers galaxy/tools/snpEff/_install_from.sh
    • gene indexes for all available genomes downloaded and install
      • 1112 genomes, 4.8G
      • data in /scratch/share/public_datasets/ngs/databases/snpEff/3_1/data
      • parallel download script /scratch/share/public_datasets/ngs/scripts/databases/snpEff/qsub_download_snpEff_genome

Pairwise Sequence Alignment

• GeneWise (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors)
  • wise2.2.0 (donload binary) NgsCctsGeneWise

Variant Handling

• vcflib https://github.com/ekg/vcflib NgsCctsVcflib
• vcftools

in process

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