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bambi

Process Illumina instrument data into SAM/BAM/CRAM files.

bdg-nextflow

Workflows implemented via Nextflow. Apache 2 licensed.

bedtk

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

binosnp

:mag: :pill: Detection of low-frequency SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains

bio

Bioinformatics library for .NET

bio.vcf

A CSharp Parser for VCF Files

bio_tools

Useful bioinformatic scripts

biodata

Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics

biofsharp

Open source bioinformatics and computational biology toolbox written in F#.

bioinformatics-workbook

Bioinformatics Workbook repository

bioprotobufparser

Fasta and gbff to protobuf converter.

biosql

cqs.core

CQS.Core

fastq2matrix

fermi-lite

Standalone C library for assembling Illumina short reads in small regions

genometools

GenomeTools genome analysis system.

gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

gsuite

Specification and example files of the GSuite tabular file format, which is part of the the GTrack ecosystem:

gtrack

The GTrack ecosystem - expressive file formats for analysis of genomic track data. Up-to-date information and specification of the GSuite file format is available here:

gtrackcore

gtrackcore: A Python package supporting parsing, conversion and operations of genomic track files.

hardware_introduction

What scienfitic programmers must know about CPUs and RAM to write fast code.

htseqqc

High-throughput sequencing (HTS) data quality control analysis software tool

kaiju

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

kalign

A fast multiple sequence alignment program.

keras_deep_clustering

How to do Unsupervised Clustering with Keras

machineboss

Bioinformatics Open Source Sequence machine

mercounting.jl

Kmer counting algorithms and count-data utilities for the BioJulia framework

microbial_amr_ml

Code repository for machine learning and computational analysis of large-scale microbial genomics data (https://rdcu.be/9rHj)

mongodb.entities

A data access library for MongoDB with an elegant api, LINQ support and built-in entity relationship management

mtbgt

The MycTBGenometoTest (MTBGT) tool transforms WGS-derived SNPs into laboratory-validated results of Xpert MTB/RIF Classic, Xpert MTB/RIF Ultra, and the LPAs GenotypeMDRTBplusv2.0 (Hain) and Genoscholar NTM + MDRTB II (Nipro).