Welcome to BACTpipe’s documentation!

BACTpipe is a complete pipeline for assembly of whole genome sequenced bacterial isolates.

BACTpipe can use a known reference genome to order and annotate assembled contigs, as well as assemble genomes of unknown species and automatically determine the best reference genome to use for contig ordering and annotation.


Authors:Abhinav Sharma, Emilio Rudbeck, Joseph Kirangwa, Sandra Alvarez-Carretero, Fredrik Boulund, Kaisa Thorell

This is the documentation for BACTpipe version 3.1.0, last updated Sep 06, 2022. The documentation is available online at https://bactpipe.readthedocs.org.

BACTpipe is published as open source under the MIT license and you are welcome to look at, suggest improvements, or download and improve/contribute to the code at the project’s Github repository page.


If you want to contribute to the development of BACTpipe, please fork the Github repository and submit a pull request.

Citing BACTpipe

If you find BACTpipe useful and publish something using BACTpipe, please cite:

Emilio Rudbeck; Abhinav Sharma; Joseph Kirangwa; Yue Hu; Sandra Álvarez-Carretero; Fredrik Boulund; Kaisa Thorell (2017-2021).
BACTpipe: bacterial whole genome sequence assembly and annotation pipeline.

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