pipesnake

pipesnake automates the processing, assembly, and phylogenetic estimation of genomic data from short-read sequences for phylogenomic reconstruction.

Key Features:

• Phylogenomic Data Processing: Processes, assembles, and estimates phylogenies from short-read sequencing data.
• Nextflow Implementation: Written in Nextflow for automated workflow execution.
• Containerized Deployment: Deployable via Docker, Singularity, and Conda for different compute infrastructures.

Scientific Applications:

• Phylogenomic Reconstruction: Facilitates phylogenomic reconstruction from conserved genomic loci at both shallow and deep evolutionary scales.
• Reproducible Phylogenetics: Supports reproducible analysis within large-scale genomics initiatives such as the Australian Amphibian and Reptile Genomics (AusARG) initiative.

Methodology:

The pipeline is written in Nextflow and processes short-read sequences for assembly and phylogenetic estimation from conserved genomic loci.