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accel-align-release

A fast seed-embed-extend based sequence mapper and aligner

accucopy

Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.

ace

Absolute Copy Number Estimation using low-coverage whole genome sequencing data

aceseqworkflow

Allele-specific copy number estimation with whole genome sequencing

almosthere

Progress indicator library written in C.

arriba

Fast and accurate gene fusion detection from RNA-Seq data

avxtoneon

Encapsulate the frequently used AVX instructions as independent modules to reduce repeated development workload.

await

28Kb, small memory footprint, single binary that run list of commands in parallel and waits for their termination

bambi

Process Illumina instrument data into SAM/BAM/CRAM files.

bamio

bamlite with bam_write added back and built-in khashl

bcfanno

A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bedtk

A simple toolset for BED files

bwa

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

bwa-mem2

The next version of bwa-mem

c-thread-pool

A minimal but powerful thread pool in ANSI C

caveman

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

cgpbigwig

BigWig manpulation tools using libBigWig and htslib

cgranges

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

chm13

The complete sequence of a human genome

complete-striped-smith-waterman-library

computer-science

:mortar_board: Path to a free self-taught education in Computer Science!

conifer

Calculate confidence scores from Kraken2 output

conliga

Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)

conta

Conta is an R package to detect cross contamination and source of contamination

cs-video-courses

List of Computer Science courses with video lectures.

ctl

The C Template Library

cuckoo-trie-code

dot_vimrc

my vimrc file and fav font

duf

Disk Usage/Free Utility - a better 'df' alternative