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 (download binary)]
** 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  
** 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)] [wiki: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-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 ]
* [http://www.ebi.ac.uk/~zerbino/velvet velvet ]
** velvet_1.2.08 (download src)([[NgsCctsBuildVelvet]])
** 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

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

Microbiome

R-packages

Alignment Visualization

Short Read Aligners

Short Read (denovo) Assemblers

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

Pairwise Sequence Alignment

Variant Handling

in process

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