Microbial Bioinformatics

Introduction

This docker image is collection of some of the most popular software and tools currently being used in the analysis of raw NGS data, genome assembly and annotation of microbial genomes. All of the software are ready to use in the docker image that can be run on any machine (e.g. Mac, Linux and Windows) or on high performance cluster/computing platform via singularity. The docker app respository is available from the docker hub.

Software

Here is the list of software available through this docker app. All of the sotware binaries are paresent in the /opt directory and soft linked to the /usr/bin for ready to use. Each of the sotware/tool standard use or manual can be accessed on providers webpages.

Raw fastq quality check and manipulation tools
- FastQC
- MultiQC
- Trimmomatic
- Cutadapt
- Trim Galore
NGS data manipulation tools
- Bcftools
- Samtools
- Htslib
- Seqkit
Fasta file alignment and fastq mapping tools
- Blast+
- ClustaW
- Mafft
- Diamond
- Mummer
- Snp-dists
- Snp-sites
- FastTree
- Bowtie2
- BWA
- Minimap2
- Lofreq
- Snippy
Genome assemblers
- Kraken2
- Spades
- Unicycler
- MIRA
- Ariba
- Quast
- Megahit
- Garm-meta
- Racon
- Shovill
- Scaffold builder
Genomes annotation tools
- Prokka
- Artemis
- Eggnog-mapper
- SnpEFF
- Vcf-annotator
Phylogenetic analysis tools
- Metaphlan
- PhyloFlash
Visualisation and other genome manipulation tools
- Ribopicker
- Barrnap
- Krona Tools
- Abricate
- Breseq
- ClonalFrameML
NGS and genome download tools
- NCBI genome download

Usage

Login account details for sudo

User: microgen

Password: bioinfo

For docker desktop (windows)

Pull image from online docker hub to local computer.

docker pull masoodzaka/microbial_bioinformatics

Create a folder to map it to docker container on your window's drive

e.g. drive(d):/microgen

Start the your contianer using following command from the latest version of docker app

docker run -d -v d:/microgen:/home/microgen \
--name microgen_container \
-it masoodzaka/microbial_bioinformatics:<tag>

Connect to the running container using following command

docker exec -i -t microgen_container

Stop the running container

docker stop microgen_container

Re-running the existing will have two steps

docker start microgen_container
docker attach microgen_container

For docker (Ubuntu)

Create a folder to map it to docker container using following command

sudo mkdir -p microgen

Start the your contianer using following command from the latest version of docker app

sudo docker run -d -v ~/microgen:/home/microgen \
--name microgen_container \
-it masoodzaka/microbial_bioinformatics:<tag>

Connect to the running container using following command

docker exec -i -t microgen_container

For HPC or Clusters

For security reasons, docker is not directory accessible on HPC or Computer clusters environment such as SGE or Slurm on private, research lab or University network. However, we can use Singularity such as this one from NIH as an ulternate for performing similar tasks. To learn more about singularity visit this documentation from Sylabs.

You can quick start singularity by pulling the docker image using following command.

singularity pull docker://masoodzaka/microbial_bioinformatics

Updates

Clone the main git repository using:

git clone https://github.com/masoodzaka/microbial_bioinformatics.git

and make a new folder with version tag:

cd microbial_bioinformatics
mkdir -p <tag>
cd <tag>
touch Dockerfile

Access the content of previous Dockerfile image using the "FROM" root container:

FROM masoodzaka/microbial_bioinformatics:latest

And build the latest docker image app using standard docker build command

docker build -t masoodzaka/microbial_bioinformatics:latest

Push the docker image

docker image push masoodzaka/microbial_bioinformatics:latest

Please report or suggest on any changes on git