BACTpipe is a whole genome sequencing workflow. It does quality assessment of paired input reads, tries to assess if the sample contains mixed or pure isolates, performs de novo assembly, and annotates the assembled genome. BACTpipe uses Nexflow as a workflow manager.
Complete documentation is available at https://bactpipe.readthedocs.io.
You need to have Nextflow and Python 3.6+ installed. The easiest way to get BACTpipe up and running is to install all other dependencies using conda. The following command installs the required software:
conda install java mash bbmap fastqc shovill multiqc
In order to run the contamination screening step, a mash screen database is required. Download it from here:
https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh
Nextflow makes it easy to run BACTpipe:
$ nextflow run ctmrbio/BACTpipe --mashscreen_database path/to/refseq.genomes.k21s1000.msh --reads 'path/to/reads/*_R{1,2}.fastq.gz'
This will run BACTpipe locally. For more details on how to run BACTpipe, see the official documentation at https://bactpipe.readthedocs.io.
BACTpipe is published under the MIT license 2018
Joseph Kirangwa (@b16joski), Sandra Alvarez-Carretero (@sabifo4), Fredrik Boulund (@boulund), Kaisa Thorell (@thorellk)