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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, however, is 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.