This repository contains Dockerfiles and additional files to build a bunch of bioinformatic tools useful for NGS data analysis. The dockerzied tools are available on dockerhub (https://hub.docker.com/u/myskmadra). Additionally, a wrapper script is provided for each tool. These scripts should enable users, unfamiliar with docker, to run the tools. The following tools are available:
- ABRicate 0.9.8
- BUSCO 3.0.2
- FastQC 0.11.5
- Flye 2.6
- Guppy 3.1.5
- KmerFinder 3.0.2
- LRE-Finder 1.0.0
- Kraken 2.0.8-beta
- MinIONQC
- mlst 2.17.6
- POCP
- Prokka 1.14.1
- QUAST 5.0.2
- Racon 1.4.7
- SPAdes 3.13.1
- Unicycler 0.4.7
To allow an easy update of the wrappers, the script generate_wrapper.sh was written which automatically writes the tool script files. It uses twor.spec, for tools without reference, and twr.spec, for tools with reference. Additional parameters are defined for each tool in tool/conf.spec. New tools need to be added to the appropriate array in generate_wrapper.sh.
MinIONQC is not part of the automated wrapper generation.
The current version of BUSCO is 3.0.2. To use the docker image, you need to download the required databases from the BUSCO website (https://busco.ezlab.org/). At the moment, the docker image does not support plotting.
MinIONQC is not versionized. It is a simple R script run in command line.