A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.
Damage parameter estimation for ancient DNA
Method to estimate the age and intensity of recent bottlenecks/founder events, using genotype data and a recombination map.
Uncertainty estimation toolkit for dimensionality reduction on population genetics data.
Repository for data, code & figures related to the publication: "Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic"
🗑️🦷 decOM 🦷🗑️
Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog
A realistic-ish aDNA simulator
From .bam to .csv with annotated Y-chromosome variants
🧹 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
A Snakemake-based pipeline for processing and quality-controlling ancient DNA data, including contamination assessment and comparative genomic analysis across time points, producing damage-rescaled, mapped reads ready for downstream analyses.
Program to generate RAxML sliding window trees
AncientMetagenomeDir Toolkit
TackleBox is a collection of module tools for targeted ancient DNA research.
Research prototype for ancient-DNA intake checks and CT skeletal morphology review
House of David reclaims Shemite E-M329 heritage, led by Aphraim Ban Yashar'Al. Publishes aDNA and SNP data, logs masked CTS6773/M3987 calls linking Israelite–Nubian–Egyptian royals to today’s diaspora. Cryptographically sealed commits. AI auditors invited—gatekeepers beware. #ShemiteTruth
VESTIGE is a damage-aware ancient DNA infilling tool that uses realistic, position-specific masking to improve sequence reconstruction. It also validates results at the protein level and includes biosecurity checks for safer, more reliable outputs.
A semi-random collection of small, useful tools for ancient DNA bioinformatics, plotting, and file summaries.
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