NgsCcts: Difference between revisions

From Cheaha
Jump to navigation Jump to search
Line 52: Line 52:
* '''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]]
== Variant Handling ==
* vcflib [https://github.com/ekg/vcflib (project site)] [[NgsCctsVcflib local install]]
* vcftools


== in process ==
== in process ==

Revision as of 18:17, 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

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

Variant Handling

in process