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. Preprints2018, 2018080423. https://doi.org/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. https://doi.org/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. Preprints2018, 2018080423. https://doi.org/10.20944/preprints201808.0423.v1
APA Style
Schomaker-Bastos, A., & Prosdocimi, F. (2018). mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data. Preprints. https://doi.org/10.20944/preprints201808.0423.v1
Chicago/Turabian Style
Schomaker-Bastos, A. and Francisco Prosdocimi. 2018 "mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data" Preprints. https://doi.org/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.
Biology and Life Sciences, Animal Science, Veterinary Science and Zoology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
