NgsCcts

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(Pairwise Sequence Alignment)
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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 (project site)] [[NgsCctsVcflib local install]]
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* vcftools
  
 
== in process ==
 
== in process ==

Revision as of 12:17, 24 February 2014

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

Pairwise Sequence Alignment

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

Variant Handling

in process

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