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 May 4, 2024, 1:56 p.m.

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MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

updated at May 3, 2024, 8:21 p.m.

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bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

updated at May 3, 2024, 4:48 p.m.

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samtools by samtools

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

updated at May 3, 2024, 1:26 a.m.

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fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

updated at May 2, 2024, 2:09 p.m.

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Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

updated at May 2, 2024, 12:20 p.m.

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seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

updated at May 2, 2024, 10:31 a.m.

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WFA2-lib by smarco

WFA-lib: Wavefront alignment algorithm library v2

updated at May 1, 2024, 1:35 p.m.

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bwa by lh3

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

updated at April 30, 2024, 10:02 p.m.

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zindex by mattgodbolt

Create an index on a compressed text file

updated at April 28, 2024, 11:13 p.m.

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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 28, 2024, 2:04 p.m.

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parasail by jeffdaily

Pairwise Sequence Alignment Library

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

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lumpy-sv by arq5x

lumpy: a general probabilistic framework for structural variant discovery

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

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wtdbg2 by ruanjue

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

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

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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.

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wgsim by lh3

Reads simulator

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

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tabix by samtools

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

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

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grabix by arq5x

a wee tool for random access into BGZF files.

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

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