danielecook/Awesome-Bioinformatics

samtools by samtools

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

created at March 9, 2012, 2:49 a.m.

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bwa by lh3

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

created at Jan. 14, 2011, 1:36 a.m.

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seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

created at March 23, 2012, 11:24 p.m.

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MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

created at July 20, 2016, 6:17 a.m.

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bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

created at Dec. 9, 2013, 9:18 p.m.

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Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

created at March 17, 2016, 10:47 p.m.

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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

created at July 12, 2013, 12:55 p.m.

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zindex by mattgodbolt

Create an index on a compressed text file

created at Feb. 26, 2015, 1:33 p.m.

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wtdbg2 by ruanjue

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

created at Sept. 29, 2017, 10:24 a.m.

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lumpy-sv by arq5x

lumpy: a general probabilistic framework for structural variant discovery

created at Oct. 8, 2012, 9:09 a.m.

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wgsim by lh3

Reads simulator

created at Jan. 22, 2011, 10:57 p.m.

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parasail by jeffdaily

Pairwise Sequence Alignment Library

created at May 21, 2015, 7:31 p.m.

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fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

created at Nov. 8, 2013, 1:03 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

created at Dec. 15, 2019, 5:23 a.m.

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WFA2-lib by smarco

WFA-lib: Wavefront alignment algorithm library v2

created at June 13, 2021, 1:32 p.m.

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tabix by samtools

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

created at March 9, 2012, 1:46 a.m.

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grabix by arq5x

a wee tool for random access into BGZF files.

created at May 22, 2012, 1:53 p.m.

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samstat by TimoLassmann

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

created at Dec. 11, 2017, 7:07 a.m.

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