Preprint Article Version 1 This version is not peer-reviewed

mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data

Version 1 : Received: 16 August 2018 / Approved: 24 August 2018 / Online: 24 August 2018 (03:24:37 CEST)

How to cite: Schomaker-Bastos, A.; Prosdocimi, F. mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data. Preprints 2018, 2018080423 (doi: 10.20944/preprints201808.0423.v1). Schomaker-Bastos, A.; Prosdocimi, F. mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data. Preprints 2018, 2018080423 (doi: 10.20944/preprints201808.0423.v1).

Abstract

Next-generation sequencing is now a mature technology, allowing partial animal genomes to be produced for many clades. Though many software exist for genome assembly and annotation, a simple pipeline that allows researchers to input raw sequencing reads in fastq format and allow the retrieval of a completely assembled and annotated mitochondrial genome is still missing. mitoMaker 1.0 is a pipeline developed in python that implements (i) recursive de novo assembly of mitochondrial genomes using a set of increasing k-mers; (ii) search for the best matching result to a target mitogenome and; (iii) performs iterative reference-based strategies to optimize the assembly. After (iv) checking for circularization and (v) positioning tRNA-Phe at the beginning, (vi) geneChecker.py module performs a complete annotation of the mitochondrial genome and provides a GenBank formatted file as output.

Supplementary and Associated Material

https://sourceforge.net/projects/mitomaker/: Source code and further information

Subject Areas

mitochondrial DNA; mitochondrial genome; genome assembly; genome annotation; next generation sequencing; animal genomics; partial genomics; bioinformatics

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