mtdna

A bioinformatics pipeline to analyze mtDNA from NGS data

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

These python scripts help you predict your Y and mtDNA haplogroup offline.

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…

Two-parameter Kimura distributions for mtDNA heteroplasmy analysis

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

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

Analyses of Penter et al., Blood Cancer Discovery 2024

Forensic mtDNA Pipeline (FMP) for NimaGen RC-PCR whole mitogenome data. A Nextflow pipeline that merges and trims the reads, removes NUMT reads with rtn, calls variants with FDSTOOLS and Mutect2, and reports both callers' calls, point and length heteroplasmy included, in one Excel table per sample.

Variant calling for the hyper-variable region of the mitochondria generated by overlapping amplicons, such as those generated by the Promega PowerSeq™ CRM Nested System.

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

Amino acid shift in mitochondrial proteins is shaped by mtDNA mutational spectrum

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

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.