DOI: 10.5061/dryad.h70rxwdt2
title: A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections

description: Low coverage “genome-skims” are often used to assemble organelle genomes
 and ribosomal gene sequences for cost-effective phylogenetic and barcoding
 studies. Natural history collections hold invaluable biological
 information, yet poor preservation resulting in degraded DNA often hinders
 PCR based analyses. However, it is possible to generate libraries and
 sequence the short fragments typical of degraded DNA to generate
 genome-skims from museum collections. Here we introduce a snakemake
 toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo,
 designed to unlock the genomic potential of historical museum specimens
 using genome skimming. Specifically, skim2mito and skim2rrna perform the
 batch assembly, annotation and phylogenetic analysis of mitochondrial
 genomes and nuclear ribosomal genes, respectively, from low-coverage
 genome skims. The third pipeline gene2phylo takes a set of gene alignments
 and performs phylogenetic analysis of individual genes, partitioned
 analysis of concatenated alignments and a phylogenetic analysis based on
 gene trees. We benchmark our pipelines with simulated data, followed by
 testing with a novel genome skimming dataset from both recent and
 historical solariellid gastropod samples. We show that the toolkit can
 recover mitochondrial and ribosomal genes from poorly preserved museum
 specimens of the gastropod family Solariellidae, and the phylogenetic
 analysis is consistent with our current understanding of taxonomic
 relationships. The generation of bioinformatic pipelines that facilitate
 processing large quantities of sequence data from the vast repository of
 specimens held in natural history museum collections will greatly aid
 species discovery and exploration of biodiversity over time, ultimately
 aiding conservation efforts in the face of a changing planet.
description: # A snakemake toolkit for the batch assembly, annotation, and phylogenetic
 analysis of mitochondrial genomes and ribosomal genes from genome skims of
 museum collections
 [https://doi.org/10.5061/dryad.h70rxwdt2](https://doi.org/10.5061/dryad.h70rxwdt2) ## Description of the data and file structure This data includes the configuration files and reference data used for the analyses of genome skimming data from Solariellidae museum collections.  ### Files and variables #### File: skim2mito\_config\_solariellid.yaml **Description:** Config file used for the skim2mito pipeline. #### File: skim2mito\_gene.fasta **Description:** Reference gene fasta used for the GetOrganelle step of the pipeline.  #### File: skim2mito\_samples\_solariellid.csv **Description:** Samples file used for the skim2mito pipeline. ##### Variables * ID: Sample ID * forward: Path to forward reads * reverse: Path to reverse reads * taxid: NCBI taxon ID * seed: Path to GetOrganelle seed reference * gene: Path to GetOrganelle gene reference #### File: skim2mito\_seed.fasta **Description:** Reference seed fasta used for the GetOrganelle step of the pipeline. #### File: skim2rrna\_config\_solariellid.yaml **Description:** Config file used for the skim2rrna pipeline. #### File: skim2rrna\_samples\_solariellid.csv **Description:** Samples file used for the skim2rrna pipeline. ##### Variables * ID: Sample ID * forward: Path to forward reads * reverse: Path to reverse reads * taxid: NCBI taxon ID * seed: Path to GetOrganelle seed reference * gene: Path to GetOrganelle gene reference #### File: skim2rrna\_rRNA.fasta **Description:** Reference gene and seed fasta used for the GetOrganelle step of the pipeline.