ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

All of pipesnake's documentation is covered in this lovingly crafted Wiki.

Antsy? Follow our Quick Start guide to get up and running (slithering?).

pipesnake comes with documentation about the pipeline usage, parameters and output.

A detailed summary of the workflow---including tools used---can be found in the Wiki.

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch. Having trouble? Open an issue or try contacting us directly.

If you use pipesnake, please consider citing it and its depenedencies. A preprint is available on bioRxiv, and a final version of the manuscript will hopefully be out soon.

pipesnake: Generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci

Brennan, I.G., Singhal, S., Al Bkhetan, Z.

doi: https://doi.org/10.1101/2024.02.13.580223

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.