Revision as of 17:33, 15 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

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 35: / Line 35: @@
 *** MAXKMERLENGTH = 57
 *** LONGSEQUENCES
-=== in process ===
+== SNP analysis ==
+* [http://snpeff.sourceforge.net/index.html SnpEff]
+** snpeff_3_1 ([http://sourceforge.net/projects/snpeff/files/snpEff_v3_1_core.zip/download zip])
+*** gene indexes for all available genomes downloaded and install
+**** 1112 genomes,
+**** 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
+== in process ==
 * [http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS] '''NOT DONE'''
 ** abyss_1.3.4 ([http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz download src])([[NgsCctsBuildAbyss]])