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
Uncertainty estimation toolkit for dimensionality reduction on population genetics data.
Method to estimate the age and intensity of recent bottlenecks/founder events, using genotype data and a recombination map.
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
Program to generate RAxML sliding window trees
AncientMetagenomeDir Toolkit
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
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