NgsCcts

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(Gene Prediction)
m (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]

Revision as of 22:54, 27 March 2013

Contents

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

  • GeneWise (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors)

in process

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