refresh-bio/VCFShark

1

KMC

Fast and frugal disk based k-mer counter

C++

268

2

agc

Assembled Genomes Compressor

C++

154

3

FAMSA

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

C++

147

4

kmer-db

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

C++

83

5

SPLASH

C++

70

6

DSRC

DSRC - DNA Sequence Reads Compressor

C++

55

7

colord

A versatile compressor of third generation sequencing reads.

C++

49

8

vclust

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

Python

48

9

PHIST

Phage-Host Interaction Search Tool

C++

27

10

Whisper

C++

24

11

ORCOM

Overlapping Reads COmpression with Minimizers

C++

16

12

GTC

GenoTypes Compressor

C++

15

13

FaStore

FaStore - high-performance FASTQ files compressor

C++

15

14

fqsqueezer

FQSqueezer - FASTQ compressor based on k-mer statistics

C++

15

15

protestar

Protein Structure Archiver

C++

12

16

RADULS

Ultra fast MSD radix sorter

C++

11

17

RECKONER

C++

8

18

GDC2

Genome Differential Compressor 2

C++

7

19

CoMSA

Compressor of multiple sequence alignments data

C

4

20

clusty

C++

4

21

GTShark

GTShark: Genotype compression in large projects

C++

3

22

LZ-ANI

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes

C++

1

23

MuGI

Multiple Genome Index

C++

1

24

QuickProbs

Accurate algorithm for the multiple sequence alignment.

C++

1