Workflows
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skim2mito
skim2mito is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.
Contents
- Setup
- Example data
- Input
- Output
- Filtering contaminants
- [Assembly and ...
gene2phylo
gene2phylo is a snakemake pipeline for batch phylogenetic analysis of a given set of input genes.
Contents
Setup
The pipeline is written in Snakemake and uses conda to install the necessary tools.
It is strongly recommended to install conda using Mambaforge. See details here ...
skim2rrna
skim2rrna is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of ribosomal genes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.
Contents
- Setup
- Example data
- Input
- Output
- Filtering contaminants
- [Assembly and annotation ...