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23andme-to-ysnps

If you have a 23andMe raw data file which contains Y-DNA data with refSNPs/RSID but not the names of Y-SNPs in ISOGG format, this tool will help you. Please note that only positions of build 37 are supported.

40d_dev

40D port of 1000d_dev from coutts

adna_to_dataset

adnapipeline

adnapipeline_parabricks

ancient-ancestry

Compare DNA segments with ancient samples!

assembly-converter

Convert human genome coordinates from one assembly to another on raw autosomal files.

autosomal-dna-converter

Conversion between the raw Autosomal DNA data from FTDNA, 23andMe, Ancestry and deCODEme formats.

bam-analysis-kit

bam-analysis-kit-linux

BAM Analysis Kit for Linux

bamutil

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

bwa-mem2

The next version of bwa-mem

cgatools

Porting Complete Genomics Analysis Tools 1.8.0 (2013) from BOOST_FILESYSTEM_VERSION v2 (deprecated in 1.48.0, 2011) to v3

clade-finder

Determines Y-Haplogroup Clade From Positive and Negative SNPs

convertmergevcf

This repository contains python scripts that utilize the liftOver python package

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

extract23

Extract a simulated 23andMe (V3) style file from a Whole Genome BAM file

falltergeist

Opensource crossplatform Fallout 2™ game engine writen in C++ and SDL. Current version: 0.2.0

fastahack

utilities for indexing and sequence extraction from FASTA files

finfamily

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

g25_ancients

G25

haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

harjoitus-pull-request

Harjoittelemme Githubia

hisat2

Graph-based alignment (Hierarchical Graph FM index)

ia32rtools

isa-l

Intelligent Storage Acceleration Library

karyo_rxry

Script for sex identification and aneuploidy detection using ancient DNA.

leehom

Bayesian reconstruction of ancient DNA fragments