cjw85

fastx

Just a python fasta/q parser based on kseq.h

myriad

Simple distributed computing in python

gpustat

📊 A simple command-line script (wrapper for nvidia-smi) for querying and monitoring GPU status

hdf5perl

HDF5 Perl Module

abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics

bri

Bam Read Index - Extract alignments from a bam file by readname

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

htslib

C library for high-throughput sequencing data formats

kseq-demo

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

minimap2

A fast pairwise aligner for genomic and spliced nucleotide sequences

nextflow

A DSL for data-driven computational pipelines

nf-batch-tag

open-data-registry

A registry of publicly available datasets on AWS

parasail-python

Python bindings for the parasail C library.

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

samtools

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

scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

spoa

SIMD partial order alignment tool/library

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

StarCluster

StarCluster is an open source cluster-computing toolkit for Amazon's Elastic Compute Cloud (EC2).

vim

wf-fun-times

whatshap

Read-based phasing of genomic variants, also called haplotype assembly