NgsCcts

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(Gene Prediction)
(Variant Handling)
 
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* '''GeneWise''' (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors)
 
* '''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]]
 
** wise2.2.0 [ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise2.2.0.tar.gz (donload binary)] [[NgsCctsGeneWise]]
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== Variant Handling ==
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* vcflib https://github.com/ekg/vcflib  [[NgsCctsVcflib]]
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* 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'''
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* [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 13:19, 24 February 2014

Contents

[edit] 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

[edit] Microbiome

[edit] R-packages

[edit] Alignment Visualization

[edit] Short Read Aligners

[edit] Short Read (denovo) Assemblers

[edit] 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

[edit] Pairwise Sequence Alignment

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

[edit] Variant Handling

[edit] in process

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