Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

The MitoGeneExtractor can be used to extract protein coding mitochondrial genes, such as COI and others from short and long read sequencing libraries.

MitoSIS (Mitochondrial Species Identification System) is a wrapper for mitochondrial genome assembly and identification of sample contamination or mislabeling.

A snakemake pipeline wrapping MitoZ and getOrganelle for de novo mitogenome assembly using short reads and subsequent QC.

Automated mitochondrial genome assembly using SRA public data

Comparing and evaluating mitogenome assemblers

Extraction of gene segments from genomes according to your gene boundary and genome dataset preparation