NgsCcts: Difference between revisions
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* bwa | * 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]] | ** 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 | |||
** 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]] | ** 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]] | ||
Revision as of 15:07, 26 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
- MOSAIK
- 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
- velvet_1.2.08 (download src)(NgsCctsBuildVelvet)
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
- 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