sstadick

nython

Build Python Extension Modules for Nim libraries.

lapper.cr

Crystal port of nim-lapper: a fast genomic intervals query library

scivs

Collection of Data Structures for working with genomic intervals

genomics-secondary-analysis-using-aws-step-functions-and-aws-batch

levenshtein-distance-benchmarks

Code for "Making rust as fast as go"

mash

Mash files together

ny_lapper

Python wrapper around nim-lapper using nython. Currently just a POC

asunk

Exploging io uring for fast fastq/a files

bcl2fastr

bcl2fastq faster

bed_cov

Small tool allowing for running bed coverage using different libraries for benchmarking

biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics

configs

My configuration files

cython_list_test

Just a small test with lists in cython

dgranges

D clone of cgranges algorithm.

fastq-rs

framework

Machine learning, computer vision, statistics and general scientific computing for .NET

gccontent-benchmark

Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)

GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

glommio

Glommio is a thread-per-core framework that aims to make the task of writing highly parallel asynchronous application in a thread-per-core architecture easier for rustaceans

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

kmer-cnt

Rust clones of https://github.com/lh3/kmer-cnt

lapper.zig

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

nextflow

A DSL for data-driven computational pipelines

nextflow-bug-report

Tiny repository to demonstrate a potential bug in nextflow

petal-decomposition

Matrix decomposition algorithms including PCA (principal component analysis) and ICA (independent component analysis)

radix-sort.cr

seq_io

FASTA and FASTQ parsing in Rust

smart_open

Utils for streaming large files (S3, HDFS, gzip, bz2...)