Germline mutations detection pipeline with long reads

Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]

Pipeline for genome assembly

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

STAR-RSEM pipeline for RNA-seq data processing

Assemblies from HPP Year 1 production

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data

Long read aligner

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Genome assembly and variant benchmarks for Chinese Quartet

Germline mutation pipeline

Pipeline for assemblies merging

Post analysis of assembly

Read-based phasing of genomic variants, also called haplotype assembly

A microsatellite instability analysis tools using NGS data

Microsatellite genotyping

An accurate GFF3/GTF lift over pipeline

Author's PyTorch implementation of TD3 for OpenAI gym tasks

An algorithm for centromere assembly using long error-prone reads

Conda recipes for the bioconda channel.

Genomic related tools

Phased assembly variant caller