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REFRESH Bioinformatics Group

README.md

Welcome

Welcome to the REFRESH Bioinformatics Group.

We are a group of researchers devoted to developing effective and efficient algorithms for complex computational biology problems.

The tools

K-mer counting and indexing, k-mer-based sequence comparison and variation discovery

Name Latest release Description GitHub★ Downloads
KMC v3.2.4 (2024.02.09) Fast disk-based k-mer counter.
Bioinformatics 10.1093/bioinformatics/btx304 Bioinformatics 31(10):1569 BMC Bioinform 14:160		 342 Bioconda GitHub
Kmer-db v2.3.1 (2025.05.20) Large-scale k-mer indexing/querying/distance estimation.
Nat Methods 10.1038/s41592-025-02701-7 BioInfo		 102 Bioconda GitHub
BKC v1.1.0 (2025.01.24) k-mer counting in barcoded FASTQ/FASTA data (10x, Visium, etc.). 4 GitHub
MKMC v1.0.0 (2026.05.14) Multi-sample KMC workflow producing k-mer count matrices and analyses. 4 GitHub
PHIST v1.2.1 (2024.08.04) Phage-Host Interaction Search Tool using shared k-mers.
Bioinformatics 10.1093/bioinformatics/btab837		 33 Bioconda
SPLASH v2.11.9 (2025.09.04) Reference-free discovery of regulated sequence variation from sequencing reads.
Nature Biotechnology 10.1038/s41587-024-02381-2		 97 Bioconda GitHub

Sequence alignment, alignment-based sequence comparison

Name Latest release Description GitHub★ Downloads
FAMSA WebInterface v2.5.2 (2026.03.23) Large-scale multiple protein sequence alignment: 3 million ABC transporters analyzed in 5 minutes and 18 GB RAM.
Nature Biotechnology 10.1038/s41587-026-03095-3 Scientific Reports 10.1038/srep33964		 275 Bioconda GitHub
QuickProbs v2.06 (2017.06.12) Multiple sequence alignment algorithm.
Scientific Reports 10.1038/srep41553 PLoS		 1 GitHub
LZ-ANI v1.2.3 (2024.11.25) Fast ANI tool for large genome sets.
Nat Methods 10.1038/s41592-025-02701-7		 13 Bioconda GitHub
CoMSA v1.1 (2018.04.12) Compressor of multiple sequence alignments.
Bioinformatics 10.1093/bioinformatics/bty619		 10 GitHub

Sequencing reads compression

Name Latest release Description GitHub★ Downloads
CoLoRd v1.2.1 (2023.12.12) Compressor for third-generation sequencing reads.
Nature Methods 2022 10.1038/s41592-022-01432-3		 53 Bioconda GitHub
DSRC v2.0.2 (2014.12.17) FASTQ compression toolkit.
Bioinformatics 2014 10.1093/bioinformatics/btu208 Bioinformatics 2011 10.1093/bioinformatics/btr014		 59 Bioconda GitHub
FaStore 0.8 (2017.07.25) High-performance short-read FASTQ compressor.
Bioinformatics 2018 10.1093/bioinformatics/bty205		 19 GitHub
FQSqueezer — Experimental high-end FASTQ compressor based on k-mer statistics.
Scientific Reports 2020 10.1038/s41598-020-57452-6		 18
ORCOM — Overlapping-reads compressor with minimizers.
Bioinformatics 2015 10.1093/bioinformatics/btu844		 16

Genome collections compression and indexing

Name Latest release Description GitHub★ Downloads
AGC v3.2.4 (2026.07.23) Assembled Genomes Compressor for collections of de novo genomes.
Bioinformatics 2023 10.1093/bioinformatics/btad097		 187 Bioconda GitHub
GDC2 v2.1 (2016.03.10) Genome Differential Compressor for genome collections.
Scientific Reports 2015 10.1038/srep11565		 8 Bioconda GitHub
MuGI v1.0 (2016.02.27) Multiple Genome Index for compressed exact/approximate queries.
PLOS ONE 2014 10.1371/journal.pone.0109384		 1 GitHub

Genotype collections compression

Name Latest release Description GitHub★ Downloads
GTShark — Genotype database compressor and reference-based sample compressor.
Bioinformatics 10.1093/bioinformatics/btz508		 3
GTC — Genotype collection compressor with fast query/decompression support.
Bioinformatics 10.1093/bioinformatics/bty023		 16
TGC v1.1 (2016.03.10) Thousands Genome Compressor / VCF compression tooling.
Bioinformatics 29(20):2572		 1
VCFShark — High-ratio VCF compressor.
Bioinformatics 10.1093/bioinformatics/btab211		 19

Clustering

Name Latest release Description GitHub★ Downloads
Clusty v1.3.0 (2026.01.28) Large-scale clustering from sparse distance/similarity matrices.
Nat Methods 10.1038/s41592-025-02701-7		 16 Bioconda GitHub
Vclust WebInterface v1.3.1 (2025.05.23) ANI calculation and clustering for viral genomes.
Nat Methods 10.1038/s41592-025-02701-7		 112 Bioconda GitHub PyPI

Short reads correction and mapping

Name Latest release Description GitHub★ Downloads
RECKONER v2.1 (2023.11.28) Illumina read error corrector based on KMC.
Scientific Reports ICMMI Bioinformatics 10.1093/bioinformatics/btw746		 10 GitHub downloads
Whisper v2.0.1 (2020.07.02) Short-read mapper/aligner.
SoftwareX 10.1016/j.softx.2021.100692 Bioinformatics 35(12):2043		 24 GitHub

Molecular structures compression

Name Latest release Description GitHub★ Downloads
ProteStAr v1.1.0 (2024.07.25) Protein structure archiver/compressor.
Bioinformatics 10.1093/bioinformatics/btae428		 16 GitHub
MDCompress v2.0.5 (2026.08.21) Compressor for molecular dynamics trajectories.
Bioinformatics 10.1093/bioinformatics/btag176		 2 GitHub

Utilities

Name Latest release Description GitHub★ Downloads
RADULS 2.0.0 Ultra-fast multithreaded MSD radix sorter.
ICMMI 2017 chapter BDAS 2017 chapter		 10

Pinned Loading

  1. KMC KMC Public

    Fast and frugal disk based k-mer counter: counts 55-mers in 36 gzipped FASTQ files totaling 614 GB (WGS paired-end reads of NA12878, Illumina HiSeq 2000) in under 1.5 h, using 12 threads, 32 GB of …

    C++ 342 85

  2. FAMSA FAMSA Public

    Algorithm for ultra-scale multiple protein sequence alignments: 3 million ABC transporters analyzed in 5 minutes and 18 GB of RAM.

    C++ 275 36

  3. colord colord Public

    A versatile compressor of third generation sequencing reads.

    C++ 53 15

  4. kmer-db kmer-db Public

    Fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, comparison): 16 million viral contigs analyzed in less than an hour.

    C++ 102 18

  5. agc agc Public

    Assembled Genomes Compressor (AGC) squeezing 290 GB of Human Pangenome Project assemblies down to <1.5 GB (>190× ratio), with sample and contig extraction in seconds.

    C++ 187 20

  6. vclust vclust Public

    Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

    Python 112 5

Repositories

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