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ctmrbio / BACTpipe

BACTpipe: An assembly and annotation pipeline for bacterial genomics
https://bactpipe.readthedocs.org
MIT License
20 stars 7 forks source link
annotation assembly bacteria bioinformatics nextflow pipeline whole-genome-sequencing

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BACTpipe

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 Nextflow as a workflow manager.

BACTpipe flowchart

Documentation

Complete documentation is available at https://bactpipe.readthedocs.io.

Quick-start

You need to have Nextflow, more specifically v21.04.0 and conda installed. When running with the default local profile all other software will be installed into local environments by conda througout the process.

Run BACTpipe

Nextflow makes it easy to run BACTpipe:

$ nextflow run ctmrbio/BACTpipe --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.

License

BACTpipe is published under the MIT license 2018-2021

Authors