Raw sequence data and analytical resources for: Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

Background
Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae).
Results
Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mit..., , , # Raw sequence data and analytical resources for \"Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic\"

This repository contains raw sequence data (Illumina MiSeq reads 150 bp) and scripts applied for all analyses performed in the paper \"Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic\" Alvarenga & D'Elia et al. 2024.

## Analytical Resources 1: Genome Assembly, Mapping, and Pilon Pipeline (MA, FH, AD - September 2021 - September 2022): *UNIX-Scripts.sh*

### Section 1: GENOME ASSEMBLY WITH NOVOPLASTY (MA - September 2021)

* **About**: Assembly of mitochondrial genomes using NOVOPlasty.
* **Requirements**: Reads (.fastq) and config files (.txt) in the working folder.
* **Contig files**: The config files can be downloaded here (
* **Parameters**: K-mer = 39, Insert Size = 550, Optional parameters = Insert Range = 1.8, Insert Range...