wga-essentials

Whole Genome Assembly (WGA) essentials tools and packages.

This docker image contains essential packages and tools for whole genome assembly and alignment. The following are the packages that are available in this docker image:

• fastqc
• jellyfish
• spades
• mummer
• samtools

Change Log 02/24:

Added the following tools

• freebayes
• bcftools
• bowtie2

Installation Guide

Docker

Follow the below links to install Docker on various operating systems

• OS X
• Linux
• Windows

The below steps worked on MacBook Pro (OS X High Sierra)

Pull docker image

$ docker pull srivathsapv/wga-essentials

Run the docker image

$ docker run -it -d -v <source_code_path>:/root/source_code srivathsapv/wga-essentials bin/bash

Note: The <source_code_path> can be your working directory in your host machine (local machine). This enables the docker container to access your local files (code and reads/reference genome files)

The above command will print a long hexadecimal string. Ex:

50c27954340f691c1e63655302a58349d48018b1610b8fe0092ba94a07e5914a

Take the first 6 characters of this string and execute

$ docker exec -it 50c279 bin/bash

This will take you to the bash of the docker container. To go inside the source code folder execute

# cd /root/source_code

Test the docker installation

Assume you have a ref.fa file in your source_code folder. Then run the following command

# samtools faidx ref.fa

If this command executes successfully, it means your setup process is complete.

Acknowledgement:

Many thanks to phizaz/bioconda from where I took the base images for python3 and miniconda.