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

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

Method to optimally select samples for validation and resequencing

A fast and sensitive gapped read aligner

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Model and predict short DNA sequence features with neural networks

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.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

De novo assembly based variant calling pipeline for Illumina short reads

Genomics Extension for SQLite

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

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Antimicrobial Resistance Identification By Assembly

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

A collection of publications on comparison of high-throughput sequencing technologies.

annotate a VCF with other VCFs/BEDs/tabixed files

A tool to circularize genome assemblies

A cool place to store your Hi-C

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

nim wrapper for htslib for parsing genomics data files

UGENE is free open-source cross-platform bioinformatics software

Predict plasmids from uncorrected long read data

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

R package for analyzing single-cell RNA-seq data

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Rapid large-scale prokaryote pan genome analysis

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

Efficient variant-call data storage and retrieval library using the TileDB storage library.

An open-access bioinformatics text

GenomeTools genome analysis system.

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

A genome browser that shows long reads and complex variants better

An ultrafast memory-efficient short read aligner

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

JavaScript VisualizationTools

Deep learning infrastructure for bioinformatics

Ultrafast sequence typing and gene detection from NGS raw reads

Collection of scripts for bacterial genomics

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

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

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

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

A modern genome browser built with JavaScript and HTML5.

Ten Quick Tips for Deep Learning in Biology

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.

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

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

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

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

Compute N50/NG50 and auN/auNG

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

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

Provide R access to the NCI Genomic Data Commons portal.

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

Reads simulator

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

Bystro genetic analysis (annotation, filtering, statistics)

Assembling the cause of phenotypes and genotypes from NGS data