NgsCcts

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(Short Read (denovo) Assemblers)
m (SNP analysis)
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** snpeff_3_1 ([http://sourceforge.net/projects/snpeff/files/snpEff_v3_1_core.zip/download zip])
 
** snpeff_3_1 ([http://sourceforge.net/projects/snpeff/files/snpEff_v3_1_core.zip/download zip])
 
*** gene indexes for all available genomes downloaded and install
 
*** gene indexes for all available genomes downloaded and install
**** 1112 genomes,  
+
**** 1112 genomes, 4.8G
 
**** 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

Revision as of 12:37, 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, 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

in process

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