miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

A genotype query interface.

BWT construction and search

A tool for bigWig files.

Accelerated kernel library for genomics

LoFreq Star: Sensitive variant calling from sequencing data

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

Flexible genotype query among 30,000+ samples whole-genome

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

A local-haplotagging-based small and structural variant caller

a wee tool for random access into BGZF files.

A C library for handling bigWig files

Structural Variant Index

SparkBWA is a new tool that exploits the capabilities of a Big Data technology as Apache Spark to boost the performance of one of the most widely adopted sequence aligner, the Burrows-Wheeler Align…

Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)

de Bruijn Graph-based read aligner

AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping a…

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Ultra-fast, high-performing structural variation (SV) detector

Utilities for Samtools ( http://samtools.sourceforge.net/ )

Bridge CEA In-House Batch Environment gives a uniform way to access external Batch scheduling systems.

Modified or extracted from other programs

A BGEN file format reader.

A simple lisp parser in c, because why not!

Alview : Alignment View for BAM files - a fast,portable tool for viewing short reads as native GUI program, command line or via webserver

Miscellaneous small programs

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