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-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]]
** 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]]


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**** data in /scratch/share/public_datasets/ngs/databases/snpEff/3_1/data
**** 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
**** 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 ==
== in process ==
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** 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]])
*** maxk=100
*** maxk=100
* [http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-analysis-software?package=VICUNA VICUNA] from Broad Institute - Viral genome denovo assembler '''NOT DONE'''
* [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]
** VICUNA_v1.2 [http://www.broadinstitute.org/software/viral/vicuna/vicuna.zip]
** V-FAT [http://www.broadinstitute.org/software/viral/vfat/vfat.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]
** 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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