REFRESH Bioinformatics Group

All

29 repositories

KMC
Public
Fast and frugal disk based k-mer counter
C++
•76•293•96•5•Updated Jul 8, 2025Jul 8, 2025
microbialSPLASH
Public
Python
•
MIT License
•0•0•0•0•Updated Jun 13, 2025Jun 13, 2025
SPLASH
Public
C++
•
GNU General Public License v3.0
•13•79•23•2•Updated Jun 10, 2025Jun 10, 2025
clusty
Public
clustering leiden sparse-matrices cd-hit set-cover single-linkage complete-linkage uclust
C++
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GNU General Public License v3.0
•2•12•3•0•Updated May 23, 2025May 23, 2025
vclust
Public
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
clustering viruses taxonomic-classification dereplication average-nucleotide-identity sequence-similarity genome-sequence bacteriophages
Python
•
GNU General Public License v3.0
•4•87•5•0•Updated May 23, 2025May 23, 2025
kmer-db
Public
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
genomics indexing k-mer sequence-similarity bioinformatics
C++
•
GNU General Public License v3.0
•18•91•12•0•Updated May 20, 2025May 20, 2025
bkc
Public
C++
•1•0•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
agc
Public
Assembled Genomes Compressor
compression genomes
C++
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MIT License
•14•166•6•2•Updated Nov 25, 2024Nov 25, 2024
LZ-ANI
Public
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
viruses genome-sequencing average-nucleotide-identity sequence-similarity bacteriophages
C++
•
GNU General Public License v3.0
•1•10•0•0•Updated Nov 25, 2024Nov 25, 2024
FAMSA
Public
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
proteomics longest-common-subsequence pfam multiple-sequence-alignment sequence-similarity guide-tree bioinformatics
C++
•
GNU General Public License v3.0
•28•158•6•1•Updated Sep 18, 2024Sep 18, 2024
PHIST
Public
Phage-Host Interaction Search Tool
bioinformatics genomics bacterial-genomes k-mers phages host-prediction
C++
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GNU General Public License v3.0
•2•27•4•0•Updated Jul 8, 2024Jul 8, 2024
protestar
Public
Protein Structure Archiver
compression proteins pdb mmcif alphafold
C++
•
GNU General Public License v3.0
•0•12•0•0•Updated Jun 11, 2024Jun 11, 2024
colord
Public
A versatile compressor of third generation sequencing reads.
compression genomics sequencing oxford-nanopore long-reads fastq-files pac-bio bioinformatics
C++
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GNU General Public License v3.0
•14•51•6•2•Updated Mar 24, 2024Mar 24, 2024
fqsqueezer
Public
FQSqueezer - FASTQ compressor based on k-mer statistics
compression ngs genome-sequencing illumina short-reads
C++
•0•16•1•0•Updated Feb 24, 2024Feb 24, 2024
RECKONER
Public
C++
•1•9•2•0•Updated Jan 26, 2024Jan 26, 2024
Whisper
Public
C++
•
GNU General Public License v3.0
•4•24•6•1•Updated Jan 25, 2024Jan 25, 2024
DSRC
Public
DSRC - DNA Sequence Reads Compressor
C++
•20•59•14•1•Updated May 20, 2022May 20, 2022
GDC2
Public
Genome Differential Compressor 2
C++
•
GNU General Public License v2.0
•4•8•1•0•Updated May 20, 2022May 20, 2022
TGC
Public
Thousands Genome Compressor
C++
•1•0•0•0•Updated May 19, 2022May 19, 2022
QuickProbs
Public
Accurate algorithm for the multiple sequence alignment.
C++
•1•1•2•0•Updated May 19, 2022May 19, 2022
MuGI
Public
Multiple Genome Index
C++
•
GNU General Public License v2.0
•1•1•1•0•Updated May 19, 2022May 19, 2022
CoMSA
Public
Compressor of multiple sequence alignments data
C
•0•5•1•0•Updated May 19, 2022May 19, 2022
GTC
Public
GenoTypes Compressor
C++
•
GNU General Public License v3.0
•8•15•2•0•Updated May 19, 2022May 19, 2022
GTShark
Public
GTShark: Genotype compression in large projects
C++
•
GNU General Public License v3.0
•4•3•2•0•Updated May 19, 2022May 19, 2022
VCFShark
Public
C++
•
GNU General Public License v3.0
•2•18•1•1•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
•8•17•4•0•Updated May 19, 2022May 19, 2022
RADULS
Public
Ultra fast MSD radix sorter
C++
•
GNU General Public License v3.0
•5•11•1•1•Updated Jun 23, 2020Jun 23, 2020