10x Genomics

single-cell-3prime-paper

supernova

10x Genomics Linked-Read Diploid De Novo Assembler

longranger

10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling

lariat

Linked-Read Alignment Tool

single-cell-3prime-snp-clustering

rust-bwa

Rust wrapper of the BWA C API

cellranger-atac

thermite

Spliced short read aligner implemented in Rust

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

supernova-chili-pepper

cellranger-dna

Single Cell DNA Copy Number Profiling

hts

biogo high throughput sequencing repository

louvain

Louvain graph clustering

pyBigWig

A python extension for quick access to bigWig and bigBed files

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

souporcell

Clustering scRNAseq by genotypes

ball-tree

A ball-tree implementation for K-NN

bwa

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

chromium-genome-paper

Analysis code from "Resolving the Full Spectrum of Human Genome Variation using Linked-Reads"

docopt.go

A command-line arguments parser that will make you smile.

go-sqlite3

sqlite3 driver for go that using database/sql

htslib

C library for high-throughput sequencing data formats

index_hopping_filter

Filter index-hopped reads from flowcell data

nanopb

Protocol Buffers with small code size

napari

napari: a fast, interactive, multi-dimensional image viewer for python

rkm

Generic k-means implementation written in Rust

samtools

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

simdeez

easy simd

sprs

sparse linear algebra library for rust

typescript-definitions