Revision as of 15:07, 26 March 2013

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

[ 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-2.1 exe_dist too old, must build from source (download src) NgsCctsBuildMosaik

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

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]

@@ Line 29: / Line 29: @@
 * bwa
 ** bwa-0.6.2 [http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbio-bwa%2Ffiles%2F&ts=1349814953&use_mirror=iweb (download src)] [[NgsCctsBuildBwa]]
+** mosaik-2.1 exe_dist too old, must build from source [https://mosaik-aligner.googlecode.com/files/MOSAIK-2.1.73-source.tar (download src)] [[NgsCctsBuildMosaik]]
 == Short Read (denovo) Assemblers ==