HapLink

HapLink

Welcome

Howdy! 🤠 And welcome to HapLink! 👋 HapLink is a command-line suite of tools to enable the exploration of viral quasispecies within a single sample. Our viral haplotype caller uses linkage disequilibrium on long sequencing reads (think Oxford Nanopore or PacBio HiFi) to identify genetic mutations that are likely conserved within a single virus particle.

This manual will cover the different ways of using HapLink, starting with a few tutorials before diving into the details of our reference section.

Getting started

Ready to dive in? 🤿 Here's a 30,000-foot view

curl -fsSL https://install.julialang.org | sh -s -- --yes
source ~/.bashrc
julia \
  --startup-file=no \
  --history-file=no \
  --quiet \
  -e 'using Pkg; Pkg.activate(;temp=true); Pkg.add(HapLink)'
echo 'export PATH=$HOME/.julia/bin:$PATH' >> $HOME/.bashrc
source ~/.bashrc

wget https://github.com/ksumngs/HapLink.jl/raw/v1.0.0/example/reference.fasta
wget https://github.com/ksumngs/HapLink.jl/raw/v1.0.0/example/sample.bam
wget https://github.com/ksumngs/HapLink.jl/raw/v1.0.0/example/sample.bam.bai

haplink variants \
  reference.fasta \
  sample.bam \
  --significance 0.5 \
  --depth 1 \
  --quality 10.0 \
  --position 0.01 \
  --frequency 0.05 \
  | tee sample.vcf

haplink consensus \
  reference.fasta \
  sample.vcf \
  | tee consensus.fasta

haplink haplotypes \
  reference.fasta \
  sample.vcf \
  sample.bam \
  --frequency 0.75 \
  | tee sample.yml

haplink sequences \
  reference.fasta \
  sample.yml \
  | tee sample.fasta