Introduction

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: contains tools for identifying variants between a NGS dataset a fasta reference sequence
  • ntvar: call nucleotide variants from a BAM file
  • aavar: call amino acid variants from a BAM file
  • codonvar: call codon variants from a BAM 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

Resources

• Website: https://phac-nml.github.io/quasitools/
• Installation: https://phac-nml.github.io/quasitools/installation/

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.

Installation

It is strongly recommended you refer to the documentation for full installation instructions. quasitools may be installed on any 64-bit Linux system from Bioconda with Conda (installation instructions):

1. Install Bioconda
2. Install the “quasitools” Bioconda package (conda install quasitools)

Contact

Eric Enns: eric.enns@canada.ca

Legal

Copyright Government of Canada 2017-2019

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.