611 Open source projects that are alternatives of or similar to Deeptools

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

Java utilities for Bioinformatics

Data intensive science for everyone.

NGLess: NGS with less work

A package for designing compact and comprehensive capture probe sets.

Official code repository for GATK versions 4 and up

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

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

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

A React web application to query and share any PostgreSQL database.

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

An open source platform for managing and analyzing biomedical big data

A faster lmm for GWAS. Supports GPU backend.

A high-performance, Pythonic language for bioinformatics

Toolkit for preparing genomes for submission to NCBI

Fast hash function for DNA sequences

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

Collection of scripts for bacterial genomics

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

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

The next version of bwa-mem

Example client programs for Saphetor's VarSome annotation API

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

Provide R access to the NCI Genomic Data Commons portal.

Python library to facilitate genome assembly, annotation, and comparative genomics

Efficient pythonic random access to fasta subsequences

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

🐳 Bio-dockers: dockerized bioinformatic tools

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

A library for manipulating bioinformatics sequencing formats in Apache Spark

Ultra-fast and memory-efficient (meta-)genome assembler

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Ultrafast sequence typing and gene detection from NGS raw reads

annotate a VCF with other VCFs/BEDs/tabixed files

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.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

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

Compute N50/NG50 and auN/auNG

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

A modern genome browser built with JavaScript and HTML5.

A comprehensive tutorial about GWAS and PRS

An open-access bioinformatics text

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

Assembling the cause of phenotypes and genotypes from NGS data

Bystro genetic analysis (annotation, filtering, statistics)

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Fast alignment and preprocessing of chromatin profiles

Method to optimally select samples for validation and resequencing

Project metadata manager for PEPs in Python

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

A fast 23andMe genome text file parser, now superseded by arv

BACNET is a Java based platform to develop website for multi-omics analysis

Predict plasmids from uncorrected long read data

Earl Grey: A fully automated TE curation and annotation pipeline

A fast and sensitive gapped read aligner

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Haplotype VCF comparison tools

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