Revision as of 16:39, 5 November 2012

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

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 17: / Line 17: @@
 == Short Read Aligners ==
+* [ tophat]
+** tophat-2.0.6 [http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.Linux_x86_64.tar.gz (binary)]
 * [http://bowtie-bio.sourceforge.net bowtie]
 ** bowtie-0.12.7 (linked from Galaxy)
+** bowtie-0.12.8 [http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F0.12.8%2F (binary)]
 * [http://bowtie-bio.sourceforge.net/bowtie2 bowtie2]
 ** bowtie2-2.0.0-beta7 [http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.0.0-beta7%2F&ts=1349813862&use_mirror=superb-dca3 (download binary)]