447 Open source projects that are alternatives of or similar to OpenGene.jl

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Official code repository for GATK versions 4 and up

Java utilities for Bioinformatics

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

(No maintenance) Detect gene fusion directly from raw fastq files

Method to optimally select samples for validation and resequencing

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

A robust model for quantitative comparison of ChIP-Seq data sets.

A simplified pipeline for ctDNA sequencing data analysis

Data intensive science for everyone.

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

Tools for working with genomic and high throughput sequencing data.

NGLess: NGS with less work

R package for analyzing single-cell RNA-seq data

UGENE is free open-source cross-platform bioinformatics software

A package for designing compact and comprehensive capture probe sets.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Tools to process and analyze deep sequencing data.

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

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

Project metadata manager for PEPs in Python

C library for high-throughput sequencing data formats

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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

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

Golang for Bioinformatics

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.

WebGL Heatmap Viewer for Big Data and Bioinformatics

A set of command line tools based on R and JavaScript.

Version 5 of the CAFE phylogenetics software

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

A Kotlin DSL and library to create and plot RNA 2D structures

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

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

Open source Java library for computational proteomics

Fast and flexible ORF finder

Mulled - Automatized Containerized Software Repository

Feature extraction algorithm for genomic data

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

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

🎯 Human transcription factor target genes.

Streamlining SLAM-seq analysis with ultra-high sensitivity

Improving genome bins through the combination of different binning programs

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

An R package for reproducible and automated ADMIXTOOLS analyses

📊 Codon usage tables in code-friendly format + Python bindings

3D printed sculpture of a DNA molecule, showing my own genome

Bystro genetic analysis (annotation, filtering, statistics)

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

Ploidy agnostic phasing pipeline and algorithm

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

Classify sequencing reads using MinHash.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Single Cell Analysis Pipelines

Compute N50/NG50 and auN/auNG

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

GRAph-based Finding of Individual Motif Occurrences