NgsCcts: Difference between revisions

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== Variant Handling ==
== Variant Handling ==

* vcflib [ (project site)] [[NgsCctsVcflib local install]]
* vcflib [[NgsCctsVcflib]]
* vcftools
* vcftools

Latest revision as of 18:19, 24 February 2014

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



Alignment Visualization

Short Read Aligners

Short Read (denovo) Assemblers

SNP analysis

  • SnpEff
    • snpeff_3_1 (zip)
      • scripted install of galaxy wrappers galaxy/tools/snpEff/
      • 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

Variant Handling

in process