Introduction

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Quasitools is a collection of tools for analysing viral quasispecies data. The following tools are currently available in quasitools:

  • aacoverage: builds an amino acid consensus and returns its coverage
  • call aavr: call amino acid mutations for a BAM file and a supplied reference file
  • call codonvar: call codon variants for a BAM file and a supplied reference file
  • call ntvar: call nucleotide variants for a BAM file and a supplied reference file
  • complexity: reports the complexity of a quasispecies using several measures
  • consensus: generate a consensus sequence from a BAM file
  • distance: measures the distance between quasispecies using angular cosine distance
  • dnds: calculates the dn/ds value for each region in a bed file
  • drmutations: identifies amino acid mutations
  • hydra: identify HIV drug resistance mutations in an NGS dataset
  • quality: perform quality control on FASTQ reads

Release

quasitools 0.7.0

This release provides greater functionality for the complexity tool, including the ability to run on aligned read data and filter out low frequency haplotypes.

Resources