refresh-bio repositories

31 repositories

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 se…
compression fasta genomes
compression fasta genomes compression-algorithm
C++
•
MIT License
•20•187•9•3•Updated Oct 5, 2026Oct 5, 2026
GDC2
Public
Genome Differential Compressor 2 (GDC2) for FASTA collections, achieving ~9,500× compression on 1000GP data at 200 MB/s, featuring 1 GB/s decompression and dire…
compression fasta compression-algorithm
compression fasta compression-algorithm genome-assembly vcf-files
C++
•
GNU General Public License v2.0
•3•8•1•0•Updated Oct 5, 2026Oct 5, 2026
MuGI
Public
Space-efficient MUlti-Genome Index (MuGI) for FASTA reference + VCF collections, squeezing 1,092 diploid human genomes (6.7 TB) into 6.5–32 GB RAM for microseco…
query compression genome
query compression genome vcf index compression-algorithm vcf-files
C++
•
GNU General Public License v2.0
•1•1•1•0•Updated Oct 5, 2026Oct 5, 2026
GTShark
Public
GTShark: Fast VCF GenoType compressor with rapid decompression and reference-based compression for external samples, squeezing a human genome down to ~65 KB.
compression vcf compression-algorithm
compression vcf compression-algorithm vcf-files geotypes
C++
•
GNU General Public License v3.0
•4•3•2•0•Updated Oct 5, 2026Oct 5, 2026
GTC
Public
Ultrafast VCF GenoType Compressor (GTC) with instant random access, shrinking the 4.3 TB HRC dataset (27k samples, 40M variants) down to under 4 GB.
compression vcf genotype
compression vcf genotype compression-algorithm vcf-files
C++
•
GNU General Public License v3.0
•8•16•2•0•Updated Oct 5, 2026Oct 5, 2026
TGC
Public
Thousands Genome Compressor (TGC) operating on stripped VCF data, squeezing an individual human genome down to ~400 KB.
compression vcf genotype
compression vcf genotype compression-algorithm vcf-files
C++
•1•1•0•0•Updated Oct 5, 2026Oct 5, 2026
VCFShark
Public
VCF file compressor reaching over 30-fold efficiency on massive genotype datasets, with processing speeds up to 100 MB/s and peak memory usage below 30 GB.
compression vcf compression-algorithm
compression vcf compression-algorithm vcf-files
C++
•
GNU General Public License v3.0
•1•19•1•1•Updated Oct 5, 2026Oct 5, 2026
MKMC
Public
The tool for creating k-mers counts matrices of many samples and computing various k-mer based statistics without need of a reference genome. The matrix may be …
C++
•
GNU General Public License v3.0
•0•4•0•0•Updated Sep 17, 2026Sep 17, 2026
RECKONER
Public
Illumina read substitution and indel error corrector. Processes human WGS 45x depth reads in about 4 hours, resulting in the reads quality similar to other top …
C++
•1•10•2•0•Updated Sep 17, 2026Sep 17, 2026
LZ-ANI
Public
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
viruses genome-sequencing average-nucleotide-identity
viruses genome-sequencing average-nucleotide-identity sequence-similarity bacteriophages
C++
•
GNU General Public License v3.0
•2•13•2•0•Updated Sep 12, 2026Sep 12, 2026
clusty
Public
Clustering tool optimized for sparse distance matrices: ~16M elements with ~190M connections clustered in minutes.
clustering leiden sparse-matrices
clustering leiden sparse-matrices cd-hit set-cover single-linkage complete-linkage uclust
C++
•
GNU General Public License v3.0
•4•16•2•1•Updated Sep 12, 2026Sep 12, 2026
vclust
Public
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
clustering viruses taxonomic-classification
clustering viruses taxonomic-classification dereplication average-nucleotide-identity sequence-similarity genome-sequence bacteriophages
Python
•
GNU General Public License v3.0
•5•111•9•0•Updated Sep 12, 2026Sep 12, 2026
QuickProbs
Public
Accurate algorithm for the multiple sequence alignment.
C++
•1•1•2•0•Updated Sep 12, 2026Sep 12, 2026
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.
bioinformatics genomics indexing
bioinformatics genomics indexing k-mer sequence-similarity
C++
•
GNU General Public License v3.0
•18•102•6•0•Updated Sep 10, 2026Sep 10, 2026
PHIST
Public
Phage-Host Interaction Search Tool
bioinformatics genomics bacterial-genomes
bioinformatics genomics bacterial-genomes k-mers phages host-prediction
C++
•
GNU General Public License v3.0
•2•33•6•0•Updated Sep 10, 2026Sep 10, 2026
FAMSA
Public
Algorithm for ultra-scale multiple protein sequence alignments: 3 million ABC transporters analyzed in 5 minutes and 18 GB of RAM.
bioinformatics proteomics longest-common-subsequence
bioinformatics proteomics longest-common-subsequence pfam multiple-sequence-alignment sequence-similarity guide-tree
C++
•
GNU General Public License v3.0
•35•273•11•2•Updated Sep 10, 2026Sep 10, 2026
mdcompress
Public
C++
•
BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Aug 21, 2026Aug 21, 2026
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 und…
C++
•
GNU General Public License v3.0
•85•341•85•5•Updated Jul 7, 2026Jul 7, 2026
SPLASH
Public
C++
•
GNU General Public License v3.0
•15•97•29•2•Updated Jul 7, 2026Jul 7, 2026
protestar
Public
Protein Structure Archiver
compression proteins pdb
compression proteins pdb mmcif alphafold
C++
•
GNU General Public License v3.0
•0•16•0•0•Updated Sep 10, 2025Sep 10, 2025
microbialSPLASH
Public
Python
•
MIT License
•0•0•0•0•Updated Jul 14, 2025Jul 14, 2025
bkc
Public
C++
•0•4•1•0•Updated May 8, 2025May 8, 2025
ref-utils
Public
C++
•
GNU General Public License v3.0
•0•0•0•0•Updated Dec 5, 2024Dec 5, 2024
colord
Public
A versatile compressor of third generation sequencing reads.
bioinformatics compression genomics
bioinformatics compression genomics sequencing oxford-nanopore long-reads fastq-files pac-bio
C++
•
GNU General Public License v3.0
•15•53•7•2•Updated Mar 24, 2024Mar 24, 2024
fqsqueezer
Public
FQSqueezer - FASTQ compressor based on k-mer statistics
compression ngs genome-sequencing
compression ngs genome-sequencing illumina short-reads
C++
•1•18•1•0•Updated Feb 24, 2024Feb 24, 2024
Whisper
Public
C++
•
GNU General Public License v3.0
•4•24•7•1•Updated Jan 25, 2024Jan 25, 2024
DSRC
Public
DSRC - DNA Sequence Reads Compressor
C++
•21•59•14•1•Updated May 20, 2022May 20, 2022
CoMSA
Public
Compressor of multiple sequence alignments data
C
•0•10•1•0•Updated May 19, 2022May 19, 2022
ORCOM
Public
Overlapping Reads COmpression with Minimizers
C++
•
GNU General Public License v2.0
•4•16•1•0•Updated May 19, 2022May 19, 2022
FaStore
Public
FaStore - high-performance FASTQ files compressor
C++
•
GNU General Public License v3.0
•7•19•4•0•Updated May 19, 2022May 19, 2022

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REFRESH Bioinformatics Group

All

31 repositories

agc

GDC2

MuGI

GTShark

GTC

TGC

VCFShark

MKMC

RECKONER

LZ-ANI

clusty

vclust

QuickProbs

kmer-db

PHIST

FAMSA

mdcompress

KMC

SPLASH

protestar

microbialSPLASH

bkc

ref-utils

colord

fqsqueezer

Whisper

DSRC

CoMSA

ORCOM

FaStore

Repositories list

31 repositories