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
 * V-FAT
 * V-Phaser & V-Profiler