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

Language: Shell - Size: 21.6 MB - Last synced: about 21 hours ago - Pushed: about 23 hours ago - Stars: 0 - Forks: 0

seppinho/mutserve

mtDNA Variant Caller

Language: Java - Size: 623 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 29 - Forks: 6

viromelab/tracespipe

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

Language: Shell - Size: 15 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 18 - Forks: 6

AKMARTIAN/mtDNA-Analysis-pipeline

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

Size: 18.6 KB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 0 - Forks: 0

alinja/snipsa

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

Language: Python - Size: 4.71 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 8 - Forks: 3

Runsheng/mitovar

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

Language: Python - Size: 2.68 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 2

mrueda/SG-Adviser-mtDNA

SRTI - web server to analyze mtDNA

Language: Perl - Size: 2.16 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

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.

Language: OpenEdge ABL - Size: 55.8 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 5 - Forks: 0

DanielRCA/MTDNA-CR

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

Language: Shell - Size: 38.1 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

seppinho/haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

Language: Java - Size: 30.4 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 71 - Forks: 24

mitoNGS/MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data

Language: Python - Size: 26.1 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 77 - Forks: 36

mtdna/haplochecker

Contamination detection workflow based on mtDNA

Size: 46.3 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

mitoclub/GlobalStructure

Language: Jupyter Notebook - Size: 85.2 MB - Last synced: 10 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

terrimporter/CO1Classifier

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

Size: 161 KB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 23 - Forks: 4

mitobench/mitoBench

The mitochondrial workbench

Language: Java - Size: 197 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 0

lbozhilova/kimura

Two-parameter Kimura distributions for mtDNA heteroplasmy analysis

Language: R - Size: 58.6 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

mnievesc/Ancient_mtDNA_Pipeline

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

Language: Shell - Size: 155 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 7 - Forks: 3

mrueda/ScrippsCall

SRTI framework to perform variant calling and prioritization of WES

Language: Perl - Size: 66.4 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

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).

Language: Perl - Size: 15.6 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

Hajibabaei-Lab/CO1testing

COI sequences files used to test the COI Classifier Web Portal

Size: 4.51 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0