 Welcome to the *pipesnake*. Let's get started. --- # Introduction **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](https://www.nextflow.io), 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](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. --- # Motivation + Project Background We developed *pipesnake* as part of the [***Aus***tralian ***A***mphibian and ***R***eptile ***G***enomics](https://ausargenomics.com/) (*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**.