Anchor chaining method for nucleotide sequences

SIMD partial order alignment tool/library

GUI for inspecting POD5 files

BWT construction and search

MHConstructor is a high-throughput, haplotype-informed, MHC-specific, short read de novo assembly method intended to further understand the role of MHC.

Immuological gene typing and annotation for genome assembly

Methylation/modified base calling separated from basecalling.

cfDNA cell type of origin estimation

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

Phased assembly variant caller

Tandem repeat genotyping and visualization from PacBio HiFi data

Parallel external memory suffix array construction

A reimplementation of the WaveFront Alignment algorithm at low memory

Proof-of-concept implementation of GWFA for sequence-to-graph alignment

hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.

Data from the Human PanGenomics Project

This repository contains R code for building a heatmap and histogram with the output of FastANI

Self-contained, multi-threaded fasta/q parser

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

FASTQ compression

PgRC: Pseudogenome based Read Compressor

Succinct Data Structure Library 2.0

A lightweight suffix-sorting library

Very fast ONT basecaller

Long-read splice alignment with high accuracy