Workflow for Decontamination of Genome Assembly of Caligus minimus

Important

This page is still under construction. Information may be incomplete or inaccurate.

Introduction

This workflow is intended for genome decontamination of Caligus minimus, a species of the Caligidae, a well-known copepod ectoparasite, from PacBio HiFi reads.

The Workflow

Flye (Kolmogorov, 2020)

Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. The flye assembler outputs polished contigs.

For more information, you can visit the repository here.

Kraken 2 (Wood, 2019)

Kraken 2 is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses that information to query a database. The database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.

For more information, you can visit the repository here.

Seqtk

Seqtk is a toolkit for processing sequences in FASTA/FASTQ files. In this workflow, it is used to generate the decontaminated assembly from the data derived from the Kraken2 classification report.

For more information, you can visit the repository here.

BioGenie

BioGenie is a complete bioinformatics tool, used in this workflow to compare the number of contigs between the contaminated and decontaminated assemblies.

For more information, you can visit the repository here.

Installation

Resolve Dependencies

The scripts are written to support Conda and SLURM in order to run on HPC systems.

To run this workflow, the use of a conda environment is recommended. To create the environment with all the dependencies:

1. Clone the repository:

git clone https://github.com/mikeph52/decontam_lice

2. Create the conda environment:

conda env create -f environment.yaml

3. If you're using SLURM, run the workflow:

sbatch workflow.sh

Acknowledgements

All data used for the development of this workflow were provided by the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) of the Hellenic Centre for Marine Research (HCMR), Heraklion, Crete. This workflow was developed and executed on the Zorbas HPC infrastructure of IMBBC-HCMR.