REFRESH Bioinformatics Group

All

29 repositories

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
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GNU General Public License v3.0
•1•53•3•0•Updated Dec 20, 2024Dec 20, 2024
ref-utils
Public
C++
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GNU General Public License v3.0
•0•0•0•0•Updated Dec 5, 2024Dec 5, 2024
SPLASH
Public
C++
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GNU General Public License v3.0
•9•73•19•1•Updated Dec 3, 2024Dec 3, 2024
KMC
Public
Fast and frugal disk based k-mer counter
C++
•72•280•94•5•Updated Nov 29, 2024Nov 29, 2024
bkc
Public
C++
•0•0•0•0•Updated Nov 27, 2024Nov 27, 2024
agc
Public
Assembled Genomes Compressor
compression genomes
C++
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MIT License
•13•158•7•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++
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GNU General Public License v3.0
•0•1•0•0•Updated Nov 25, 2024Nov 25, 2024
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++
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GNU General Public License v3.0
•17•85•11•0•Updated Nov 25, 2024Nov 25, 2024
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
•1•4•2•0•Updated Nov 25, 2024Nov 25, 2024
microbialSPLASH
Public
Python
•0•0•0•0•Updated Nov 21, 2024Nov 21, 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++
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GNU General Public License v3.0
•25•152•4•0•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•3•0•Updated Jul 8, 2024Jul 8, 2024
protestar
Public
Protein Structure Archiver
compression proteins pdb mmcif alphafold
C++
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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•49•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•15•1•0•Updated Feb 24, 2024Feb 24, 2024
RECKONER
Public
C++
•1•9•2•0•Updated Jan 26, 2024Jan 26, 2024
Whisper
Public
C++
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GNU General Public License v3.0
•4•24•6•1•Updated Jan 25, 2024Jan 25, 2024
DSRC
Public
DSRC - DNA Sequence Reads Compressor
C++
•19•56•15•1•Updated May 20, 2022May 20, 2022
GDC2
Public
Genome Differential Compressor 2
C++
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GNU General Public License v2.0
•4•7•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++
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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•4•0•0•Updated May 19, 2022May 19, 2022
GTC
Public
GenoTypes Compressor
C++
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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++
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GNU General Public License v3.0
•4•3•2•0•Updated May 19, 2022May 19, 2022
VCFShark
Public
C++
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GNU General Public License v3.0
•2•18•1•1•Updated May 19, 2022May 19, 2022
ORCOM
Public
Overlapping Reads COmpression with Minimizers
C++
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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++
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GNU General Public License v3.0
•7•15•4•0•Updated May 19, 2022May 19, 2022
RADULS
Public
Ultra fast MSD radix sorter
C++
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GNU General Public License v3.0
•5•11•1•1•Updated Jun 23, 2020Jun 23, 2020