NgsCcts

From UABgrid Documentation
(Difference between revisions)
Jump to: navigation, search
m (SNP analysis)
(SNP analysis)
Line 40: Line 40:
 
* [http://snpeff.sourceforge.net/index.html SnpEff]
 
* [http://snpeff.sourceforge.net/index.html SnpEff]
 
** 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])
 +
*** scripted install of galaxy wrappers [https://projects.uabgrid.uab.edu/galaxy/browser/tools/snpEff/_install_from.sh galaxy/tools/snpEff/_install_from.sh]
 
*** gene indexes for all available genomes downloaded and install
 
*** gene indexes for all available genomes downloaded and install
 
**** 1112 genomes, 4.8G
 
**** 1112 genomes, 4.8G

Revision as of 11:42, 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)
      • 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

in process

Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox