NgsCcts: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
|||
| Line 35: | Line 35: | ||
*** MAXKMERLENGTH = 57 | *** MAXKMERLENGTH = 57 | ||
*** LONGSEQUENCES | *** 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''' | * [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]]) | ** abyss_1.3.4 ([http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz download src])([[NgsCctsBuildAbyss]]) | ||
Revision as of 17:33, 15 March 2013
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
R-packages
Alignment Visualization
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
Short Read (denovo) Assemblers
- velvet
- velvet_1.2.08 (download src)(NgsCctsBuildVelvet)
- MAXKMERLENGTH = 57
- LONGSEQUENCES
- velvet_1.2.08 (download src)(NgsCctsBuildVelvet)
SNP analysis
- SnpEff
- snpeff_3_1 (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
- gene indexes for all available genomes downloaded and install
- snpeff_3_1 (zip)
in process
- ABySS NOT DONE
- abyss_1.3.4 (download src)(NgsCctsBuildAbyss)
- maxk=100
- abyss_1.3.4 (download src)(NgsCctsBuildAbyss)
- VICUNA from Broad Institute - Viral genome denovo assembler NOT DONE