COI sequences files used to test the COI Classifier Web Portal
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Updated
Jun 27, 2018
COI sequences files used to test the COI Classifier Web Portal
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).
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…
Contamination detection workflow based on mtDNA
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Mapping of RNAseq data on reference genome using Hisat2 for reduced mismatch penalties
SRTI - web server to analyze mtDNA
The mitochondrial workbench
SRTI framework to perform variant calling and prioritization of WES
Mitochondrial DNA sequence assembly and annotation for nematodes using NGS data.
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.
Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improvements.
Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)
A bioinformatics pipeline to analyze mtDNA from NGS data
This page is contains all the software and commands I've used for my mtDNA analysis.
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