AWinK

This is a stand-alone repository for executing AWinK in your local machine. AWinK is developed as a part of a project on improving de novo genome assembly in presence of ultra-deep sequencing data.

Pre-requisites

You will need conda installed in your machine to proceed. If you don't have conda installed, please follow conda installation. If you already had it installed, please make sure it is updated.

Create a conda environment first:

conda create -n awink python=3.8 numpy xlsxwriter biopython

This will create a conda environment named awink with the afforementioned packages. Then activate the environment with:

conda activate awink

Finally, install the following packages inside the newly created environment using the commands below:

conda install -c bioconda jellyfish
conda install -c bioconda minimap2
conda install -c bioconda bwa
conda install -c bioconda samtools
conda install -c bioconda pysam
conda install -c bioconda hifiasm
conda install -c bioconda seqkit

Scripts

extractUnikmers.sh contains the required commands to perform step A (Extract unikmers) read2UnikmerMap.py contains the required functions to perform step B (Barcode reads)
awink.py contains the required fucntions to execute AWinK's steps C and D (Assign reads to bins and Select reads)
assembly.sh contains the required commands to assemble the AWinK selected reads using hifiasm (step E: Assemble reads)

Execution

Open the terminal and follow the steps below to run AWinK from scratch:

  cd ~
  git clone https://github.com/anonymous/AWinK.git
  cd AWinK/scripts
  bash extractUnikmers.sh prefix k
  python read2UnikmerMap.py
  python awink.py
  bash assembly.sh

Executing the above commands one-by-one will generate the final assembly inside the user-specified hifiasm output directory with the filename $PREFIX.asm.fasta