639 Open source projects that are alternatives of or similar to reg-gen

A package for designing compact and comprehensive capture probe sets.

Tools to process and analyze deep sequencing data.

Official code repository for GATK versions 4 and up

CWL tools and workflows for GGR

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Java utilities for Bioinformatics

Data intensive science for everyone.

NGLess: NGS with less work

A genome browser that shows long reads and complex variants better

Proof-of-concept seq-to-graph mapper and graph generator

🔬 BEDOPS: high-performance genomic feature operations

Reads simulator

Ten Quick Tips for Deep Learning in Biology

Intuitive local web frontend for the BLAST bioinformatics tool

GenomeTools genome analysis system.

JavaScript VisualizationTools

Bystro genetic analysis (annotation, filtering, statistics)

Haplotype VCF comparison tools

Collection of scripts for bacterial genomics

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

chromatin Variability Across Regions (of the genome!)

Multi-omics analysis protocols by Lyu.

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Method to optimally select samples for validation and resequencing

A library for manipulating bioinformatics sequencing formats in Apache Spark

An open-access bioinformatics text

Rapid large-scale prokaryote pan genome analysis

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Deep learning infrastructure for bioinformatics

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

A powerful open source data warehouse system

A simple command-line tool to download data from Joint Genome Institute databases

🐳 Bio-dockers: dockerized bioinformatic tools

Provide R access to the NCI Genomic Data Commons portal.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Tools for working with genomic and high throughput sequencing data.

Official git repository for Biopython (originally converted from CVS)

cython + htslib == fast VCF and BCF processing

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

An ultrafast memory-efficient short read aligner

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Assembling the cause of phenotypes and genotypes from NGS data

R package for analyzing single-cell RNA-seq data

Fast hash function for DNA sequences

Ultrafast sequence typing and gene detection from NGS raw reads

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Analysing Capture Seq Count Data

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Simple pure Python SAM parser and objects for working with SAM records

Compute N50/NG50 and auN/auNG

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Toolkit for preparing genomes for submission to NCBI

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`