NgsCcts

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(Short Read (denovo) Assemblers)
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*** MAXKMERLENGTH = 57
 
*** MAXKMERLENGTH = 57
 
*** LONGSEQUENCES
 
*** LONGSEQUENCES
=== in process ===
+
 
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== SNP analysis ==
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* [http://snpeff.sourceforge.net/index.html SnpEff]
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** snpeff_3_1 ([http://sourceforge.net/projects/snpeff/files/snpEff_v3_1_core.zip/download zip])
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*** gene indexes for all available genomes downloaded and install
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**** 1112 genomes,
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**** data in /scratch/share/public_datasets/ngs/databases/snpEff/3_1/data
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**** parallel download script /scratch/share/public_datasets/ngs/scripts/databases/snpEff/qsub_download_snpEff_genome
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== in process ==
 
* [http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS] '''NOT DONE'''
 
* [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]])
 
** abyss_1.3.4 ([http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz download src])([[NgsCctsBuildAbyss]])

Revision as of 12:33, 15 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)
      • gene indexes for all available genomes downloaded and install
        • 1112 genomes,
        • 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

in process

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