GNU General Public License, GPLv3
Patchwork is an alignment-based program for retrieving and concatenating phylogenetic markers from whole-genome sequencing (WGS) data. The program searches the provided DNA query contigs against one or more amino acid reference sequences. Multiple, overlapping hits are merged to derive a single, continuous sequence for each reference sequence.
Features
- Align nucleotide sequences to one or more protein sequences
- Works with already assembled contigs or raw reads
- Stitch overlapping or gappy sequences together based on a reference
- Find homologs, even in distantly-related taxa
- 🐇 Written in Julia and utilizing DIAMOND for maximum speed
Graphical Overview
Quick installation
We are currently working on a Conda build. In the future,
the user will be able to install this program by running conda install -c bioconda patchwork. Until then, please refer to
these instructions
for installing from source. It is now also possible to install
Patchwork using Docker.
Documentation
Please see our Wiki.
Cite
Thalén, F., Köhne, C. G., & Bleidorn, C. (2023). Patchwork: alignment-based retrieval and concatenation of phylogenetic markers from genomic data. Genome Biology and Evolution, 15(12), evad227.
BibTeX-format:
@article{thalen2023patchwork,
title={Patchwork: alignment-based retrieval and concatenation of phylogenetic markers from genomic data},
author={Thal{\'e}n, Felix and K{\"o}hne, Clara G and Bleidorn, Christoph},
journal={Genome Biology and Evolution},
volume={15},
number={12},
pages={evad227},
year={2023},
publisher={Oxford University Press US}
}