mtdna
There are 24 repositories under mtdna topic.
mitoNGS/MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
seppinho/haplogrep-cmd
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
seppinho/mutserve
mtDNA Variant Caller
terrimporter/CO1Classifier
This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.
viromelab/tracespipe
Reconstruction and analysis of viral and host genomes at multi-organ level
alinja/snipsa
Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improvements.
mitobench/mitoBench
The mitochondrial workbench
mnievesc/Ancient_mtDNA_Pipeline
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
mnievesc/ENAH_curso_aDNA_2019
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-line experience needed.
Runsheng/mitovar
Mitochondrial DNA sequence assembly and annotation for nematodes using NGS data.
lbozhilova/kimura
Two-parameter Kimura distributions for mtDNA heteroplasmy analysis
ARNTET/Illumina_plant_mtDNA_assembly
Mitochondrial genome assembly using Illumina MiSeq paired-end reads
ARNTET/Pacbio_Illumina_mtDNA_assembly
Mitochondrial genome assembly combining Pacbio SMRT and Illumina MiSeq paired-end technologies
ARNTET/RNAseq_mapping_hisat2
Mapping of RNAseq data on reference genome using Hisat2 for reduced mismatch penalties
DanielRCA/MTDNA-CR
Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)
DanielRCA/NCR-mtDNA_ampliconbasedngs
A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods
Hajibabaei-Lab/CO1testing
COI sequences files used to test the COI Classifier Web Portal
liviuspenter/mtDNA_donor_recipient_coevolution
Analyses of Penter et al., Blood Cancer Discovery 2024
mtdna/haplochecker
Contamination detection workflow based on mtDNA
AKMARTIAN/mtDNA-Analysis-pipeline
This page is contains all the software and commands I've used for my mtDNA analysis.
mrueda/ScrippsCall
SRTI framework to perform variant calling and prioritization of WES
mrueda/SG-Adviser-mtDNA
SRTI - web server to analyze mtDNA
terrimporter/JesseHoage2018
This repository contains the scripts used to process Illumina MiSeq 18S, ITS2, and CO1 metabarcodes for Jesse Hoage's Master's thesis (2018). The ammended CO1 reference set is also included here (CO1 Classifier v2.1).