Software program for generating synthetic datasets for genotypes and phenotypes

A versatile pairwise aligner for genomic and spliced nucleotide sequences

C library for high-throughput sequencing data formats

A new implementation of my graph indexer, I wanted to start from scratch. Now using a different Louvain Method implementation that uses much less memory.

Constructs segment repeat-free founder block graphs from multiple sequence alignments

Mummer alignment tool

BWT-based index for graphs

An OTF math font matching the EB Garamond.

A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models.

Succinct Data Structure Library 3.0

An accurate aligner of long reads to a variation graph, based on co-linear chaining

Compacted and colored de Bruijn graph construction and querying

pangenome from maximal blocks in an MSA

AlfaPang builds pangenome graphs without alignments or references.

ALPACA/PANGAIA ANNUAL WORKSHOP - Hackathon

strange cross-platform, performance-oriented and interactive pangenome and large graph visualization

Convert PDF to HTML without losing text or format.

Identification of transposable element families from pangenome polymorphisms

Sequence-to-graph mapper and graph generator

Compressed text index supporting flexible search, such as count, locate with some mismatched characters

Compressed text index supporting complex queries, based on RLBWT.

EMERALD calculates safety-windows by exploring the suboptimal alignment space

Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.

MEM finding on texts and graphs using bidirectional r-index

Anchor chaining method for nucleotide sequences

Succinct Data Structure Library 2.0

The MiniZinc compiler