Mapping of RNAseq data on reference genome using Hisat2 for reduced mismatch penalties
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Updated
Dec 2, 2020 - Shell
Mapping of RNAseq data on reference genome using Hisat2 for reduced mismatch penalties
SRTI - web server to analyze mtDNA
COI sequences files used to test the COI Classifier Web Portal
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)
The mitochondrial workbench
Contamination detection workflow based on mtDNA
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…
Mitochondrial DNA sequence assembly and annotation for nematodes using NGS data.
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improvements.
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
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