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anchors-in-chaining

bdbwt

Bidirectional Burrows-Wheeler index

bdbwt-mem-chaining

br-index-mems

MEM finding on texts and graphs using bidirectional r-index

bwtcluster

Space-efficient clustering for metagenomic reads

efg-mems

MEM finding on (elastic founder) graphs

emerald

EMERALD calculates safety-windows by exploring the suboptimal alignment space

emerald-analysis

flow-decomposition-safety

founderblockgraphs

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

ggcat

Compacted and colored de Bruijn graph construction and querying

graphchainer

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

graphchainer-scripts

greedysuperstring

Greedy space-efficient construction of short approximate superstrings

introduction-to-applied-bioinformatics

Genome assembly - From theory to practice (and back)

kmc

A fork of KMC used in the SBWT repository https://github.com/algbio/SBWT

matchtigs

Minimum plain text representation of kmer sets

metaflow

MetaFlow is a program for community profiling of a metagenomic sample

mfd-ilp

Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.

mfd-safety

optimized-fd

panvc-founders

Instructions and examples for using PanVC with founder sequences

panvc-sample-workflow

Sample variant calling workflow using short reads for PanVC

panvc3-experiments

Experiments for evaluating PanVC 3

performancempc

practical-omnitigs

A repository to conduct experiments with omnitig-related models for genome assembly.

robustflowdecomposition

Flow Decomposition Under Uncertainty

safepathsrnapc

sbwt

Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)

sdsl-lite

Fork of Succinct Data Structure Library 2.0 used in Themisto