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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.
We developed pipesnake as part of the Australian Amphibian and Reptile Genomics (AusARG) initiative. AusARG is a national collaborative project aiming to facilitate the development of genomics resources for Australia's unique amphibian and reptile fauna. This pipeline was developed specifically as part of the AusARG Phylogenomics Working Group with the goal of collecting a consistent set of phylogenomic data for all of Australia's frogs and reptiles, under similar assembly, alignment, and tree estimation procedures.
pipesnake is however, applicable to much broader phylogenomic questions, and is appropriate for processing exon-capture or transcriptomic data, so long as the input is second-generation (short-read) data.