NgsCcts

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(Pairwise Sequence Alignment)
(Variant Handling)
 
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== Variant Handling ==
 
== Variant Handling ==
  
* vcflib [https://github.com/ekg/vcflib (project site)] [[NgsCctsVcflib local install]]
+
* vcflib https://github.com/ekg/vcflib [[NgsCctsVcflib]]
 
* vcftools
 
* vcftools
  

Latest revision as of 12:19, 24 February 2014

Contents

[edit] 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

[edit] Microbiome

[edit] R-packages

[edit] Alignment Visualization

[edit] Short Read Aligners

[edit] Short Read (denovo) Assemblers

[edit] 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

[edit] Pairwise Sequence Alignment

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

[edit] Variant Handling

[edit] in process

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