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Kelly Blevins (Kelzor)

Kelzor

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Location:Durham University

Twitter:@blevinske

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ACStoneLab

Kelly Blevins's starred repositories

Guide-to-manipulating-PLINK-EIG-and-VCF-files

A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.

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snpit

A tool for speciating M. tuberculosis isolates from WGS

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schmutzi

Maximum a posteriori estimate of contamination for ancient samples

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EIG

Eigen tools by Nick Patterson and Alkes Price lab

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AuthentiCT

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BREADR

Estimates degrees of relatedness (up to the second degree) for extrememly low-coverage data

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corephylo

core genome phylogenies

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ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

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ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

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applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

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mixs

Minimum Information about any (X) Sequence” (MIxS) specification

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KapCopenhagen

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ctv-archaeology

CRAN Task View: Archaeological Science

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aMeta

Ancient microbiome snakemake workflow

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mtbc_analyses

Code for genomics analysis of MTBC locii.

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snp_extraction_from_alignments

This repository contains tools for the extraction of Single Nucleotide Polymorphisms (SNPs) from multiple sequence alignments.

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oneliners

Useful bash one-liners for bioinformatics.

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fqgrep

Grep for FASTQ files

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admixtools

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bioinformatics

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AGAR2022_Reproducible_Genome_Assembly

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agar22

AGAR Workshop, 2022

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GLIMPSE

Low Coverage Calling of Genotypes

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popgen-notes

Population genetics notes

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maximum-likelihood-relatedness-estimation

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GenoCaller_indent

aDNA_GenoCaller is a python program that calls genotypes from bam files at positions/regions specified in a bam file while ignoring a user-specified number of bases at the ends of reads

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mapache

mapping pipeline for ancient DNA

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sam2lca

Lowest Common Ancestor from a SAM/BAM/CRAM alignment file

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aDNA-BAMPlotter

aDNA BAM plotter script for microbial genomes

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AdmixTools

Tools test whether admixture occurred and more

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