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Richard's starred repositories

ropebwt3

The construction and utility of BWT for DNA string sets

Language:C500

libtree

ldd as a tree

Language:CMIT240600

ULTRA

ULTRA Locates Tandemly Repetitive Areas

Language:C++BSD-3-Clause2100

iSeq

Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

Language:ShellMIT5200

poasta

Fast and exact gap-affine partial order alignment

Language:RustBSD-3-Clause3500

MEMO

MEMO: MEM-based pangenome indexing for k-mer queries

Language:PythonMIT1000

vcpkg

C++ Library Manager for Windows, Linux, and MacOS

Language:CMakeMIT2198800

kraken2-rust

kraken2 rust

Language:RustMIT600

python-isal

Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library.

Language:PythonNOASSERTION4000

syotti

Minimum Bait Cover Toolkit Syotti.

Language:C++GPL-2.0900

taskflow

A General-purpose Parallel and Heterogeneous Task Programming System

Language:C++NOASSERTION967200

khashl

Generic hash table library in C

Language:C1500

tpl

tpl - a small binary serialization library for C

Language:CNOASSERTION36400

await

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

Language:CMIT12800

neco

Concurrency library for C (coroutines)

Language:CMIT105100

taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Language:NextflowMIT10000

Movi

Fast and cache-efficient full-text pangenome index

Language:C++GPL-3.02300

multiply

Multiplex PCR design, in silico

Language:PythonMIT1100

gw

Genome browser and variant annotation

Language:C++MIT14400

blast-validate

BLAST-based validation of metagenomic sequence assignments

Language:Perl700

sierra

HIVDB Genotypic Resistance Interpretation Program

Language:JavaGPL-3.01400

llm.c

LLM training in simple, raw C/CUDA

Language:CudaMIT2065600

mpd-c

Multiplex Primer Design

Language:CGPL-3.02000

kent-core

All UCSC Genome Browser source code that is under an open source license, mostly file format converters, command line tools and C libraries. A subset of the "kent" repo, updated every three weeks.

Language:CMIT700

taxon-utils

utils for NCBI taxonomy manipulation

Language:CMIT100

ViennaRNA

The ViennaRNA Package

Language:CNOASSERTION27600

phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Language:CGPL-3.016600

lvgl

Embedded graphics library to create beautiful UIs for any MCU, MPU and display type.

Language:CMIT1540200

panqc

A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses

Language:PythonMIT1300

wak

wak -- an awk implementation for toybox and standalone

Language:C0BSD5100