Barcode Gene Extractor & Evaluator (BGEE) Snakemake workflow

Snakemake workflow for recovering high-quality barcode sequences from genome skim data, built around MitoGeneExtractor and adapted for genome skims of museum specimens.

Contents

• Requirements
• Workflow
• Running
• Cluster configuration
• Results structure
• Integrated and supplementary scripts ...

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 ...

This is an inclusive collection of workflows related to biodiversity and ecology (especially non-microbial). A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). It also aims at collating workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and ...