MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

updated at April 27, 2024, 6:14 p.m.

31 +0

1,256 +9

179 +0

bcftools by samtools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

updated at April 27, 2024, 5:53 p.m.

48 +0

620 +1

237 +1

bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

updated at April 27, 2024, 4:12 p.m.

58 +0

898 +0

283 +1

samtools by samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

updated at April 27, 2024, 3:44 a.m.

101 +0

1,549 +3

570 +1

bwa by lh3

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

updated at April 25, 2024, 6:27 p.m.

107 +1

1,453 +10

544 +2

zindex by mattgodbolt

Create an index on a compressed text file

updated at April 25, 2024, 3:47 p.m.

23 +0

614 +1

41 +0

Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

updated at April 25, 2024, 11:54 a.m.

28 +0

726 +1

160 +1

seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

updated at April 25, 2024, 6:08 a.m.

62 +0

1,312 +2

307 +1

parasail by jeffdaily

Pairwise Sequence Alignment Library

updated at April 25, 2024, 5:52 a.m.

18 +0

233 +1

34 +0

WFA2-lib by smarco

WFA-lib: Wavefront alignment algorithm library v2

updated at April 24, 2024, 4:32 a.m.

13 +0

142 +3

29 +0

lumpy-sv by arq5x

lumpy: a general probabilistic framework for structural variant discovery

updated at April 23, 2024, 8:49 p.m.

27 +0

299 +1

118 +0

wtdbg2 by ruanjue

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

updated at April 23, 2024, 11:16 a.m.

31 -1

493 +1

89 +0

genozip by divonlan

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

updated at April 21, 2024, 1:22 p.m.

1 +0

148 +0

10 +0

samstat by TimoLassmann

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

updated at April 12, 2024, 3:15 a.m.

3 +0

23 +0

7 +0

wgsim by lh3

Reads simulator

updated at April 11, 2024, 5:08 p.m.

17 +0

248 +0

89 +0

tabix by samtools

Note: tabix and bgzip binaries are now part of the HTSlib project.

updated at April 11, 2024, 6:37 a.m.

22 +0

91 +0

40 +0

fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

updated at March 26, 2024, 9:55 a.m.

18 +0

155 +0

60 +0

grabix by arq5x

a wee tool for random access into BGZF files.

updated at Dec. 26, 2023, 1:21 a.m.

6 +0

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12 +0