NgsCcts: Difference between revisions
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== Microbiome == | == Microbiome == | ||
* [[QIIME 1.5]] | * [[QIIME 1.5]] | ||
== R-packages == | |||
* [[R-packages]] | |||
== Alignment Visualization == | == Alignment Visualization == | ||
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== Short Read Aligners == | == 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] | * [http://bowtie-bio.sourceforge.net bowtie] | ||
** bowtie-0.12.7 (linked from Galaxy) | ** 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] | * [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 | ** 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)] | ||
* 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 | |||
** mosaik-1.1.0021 - installed in galaxy | |||
** 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 == | == Short Read (denovo) Assemblers == | ||
* [http://www.ebi.ac.uk/~zerbino/velvet velvet ] | |||
** velvet_1.2.08 ([http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.08.tgz download src])([[NgsCctsBuildVelvet]]) | |||
*** MAXKMERLENGTH = 57 | |||
*** LONGSEQUENCES | |||
== 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]) | |||
*** scripted install of galaxy wrappers [https://projects.uabgrid.uab.edu/galaxy/browser/tools/snpEff/_install_from.sh 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 | |||
== Pairwise Sequence Alignment == | |||
* '''GeneWise''' (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors) | |||
** wise2.2.0 [ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise2.2.0.tar.gz (donload binary)] [[NgsCctsGeneWise]] | |||
== Variant Handling == | |||
* vcflib https://github.com/ekg/vcflib [[NgsCctsVcflib]] | |||
* vcftools | |||
== 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]]) | |||
*** maxk=100 | |||
* [http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-analysis-software?package=VICUNA VICUNA] from Broad Institute ([[NgsCctsBuildVicuna]]) - Viral genome denovo assembler '''NOT DONE''' | |||
** VICUNA_v1.2 [http://www.broadinstitute.org/software/viral/vicuna/vicuna.zip] | |||
** V-FAT [http://www.broadinstitute.org/software/viral/vfat/vfat.zip] | |||
** V-Phaser & V-Profiler [http://www.broadinstitute.org/software/viral/v_phaser/v_phaser.zip] | |||
Latest revision as of 18:19, 24 February 2014
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-1.1.0021 - installed in galaxy
- 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)
Pairwise Sequence Alignment
- GeneWise (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors)
- wise2.2.0 (donload binary) NgsCctsGeneWise
Variant Handling
- vcflib https://github.com/ekg/vcflib NgsCctsVcflib
- vcftools
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 (NgsCctsBuildVicuna) - Viral genome denovo assembler NOT DONE