A bioinformatics pipeline to analyze mtDNA from NGS data

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

mtDNA Variant Caller

This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

Reconstruction and analysis of viral and host genomes at multi-organ level

Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improvements.

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

The mitochondrial workbench

This repository contains practical data analyses exercises for the special course on Paleogenomics and Anthropology held at the National School of Anthropology of Mexico (ENAH), May 6 to 10, 2019. Topics include performing QC on aDNA NGS data, assigning mtDNA haplogroups and testing hypotheses w/PCA and ADMIXTURE analyses. No previous command-li…

Mitochondrial DNA sequence assembly and annotation for nematodes using NGS data.

Two-parameter Kimura distributions for mtDNA heteroplasmy analysis

SRTI - web server to analyze mtDNA

This page is contains all the software and commands I've used for my mtDNA analysis.

SRTI framework to perform variant calling and prioritization of WES

Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)

A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods

Mapping of RNAseq data on reference genome using Hisat2 for reduced mismatch penalties

Y-DNA and mtDNA Haplotyping for WeGene, It features DFS algorithm and specific rules to search the most appropriate terminal haplotype based on haplogroup tree which should contain SNP information with position and derived mutation.

COI sequences files used to test the COI Classifier Web Portal