slw287r

bamio

bamlite with bam_write added back and built-in khashl

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

AvxToNeon

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

bwa

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

C-Thread-Pool

A minimal but powerful thread pool in ANSI C

CHM13

The complete sequence of a human genome

computer-science

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

cuckoo-trie-code

eu-tire-label

EU Tire Label generator (EC/1222/2009, EU/2020/740)

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

greatest

A C testing library in 1 file. No dependencies, no dynamic allocation. ISC licensed.

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

isa-l

Intelligent Storage Acceleration Library

K2Mem

K2Mem is a variant of Kraken 2 taxonomic sequence classification system that can learn from the previous classifications.

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

kff-cpp-api

A C++ API to read and write kff files

kraken2

The second version of the Kraken taxonomic sequence classification system

libBigWig

A C library for handling bigWig files

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

pandora

Pan-genome inference and genotyping with long noisy or short accurate reads

QDNAseq

QDNAseq package for Bioconductor

rascal

R package and Shiny app providing functions for scaling relative copy number to absolute values for shallow whole genome sequencing of cancer samples.

reproduce_lucas_wflow

single_file_libs

List of single-file C/C++ libraries.

sqlite3s

sqlite3 lib with secure support

SqueezeMeta

A complete pipeline for metagenomic analysis

taxonomy-tools

C++ tools for NCBI taxonomy tasks

zlib

A massively spiffy yet delicately unobtrusive compression library.