569 Open source projects that are alternatives of or similar to Hicexplorer

Predict plasmids from uncorrected long read data

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

An open source platform for managing and analyzing biomedical big data

A modern genome browser built with JavaScript and HTML5.

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.

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

Code examples of fast and simple k-mer counters for tutorial purposes

nim wrapper for htslib for parsing genomics data files

A tool to circularize genome assemblies

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

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

Rapid large-scale prokaryote pan genome analysis

A fast 23andMe genome text file parser, now superseded by arv

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

GenomeTools genome analysis system.

A collection of scripts and notes related to genomics and bioinformatics

A genome browser that shows long reads and complex variants better

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

🔬 BEDOPS: high-performance genomic feature operations

cython + htslib == fast VCF and BCF processing

Deep learning infrastructure for bioinformatics

A faster lmm for GWAS. Supports GPU backend.

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

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

Haplotype VCF comparison tools

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

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

NGLess: NGS with less work

Earl Grey: A fully automated TE curation and annotation pipeline

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Antimicrobial Resistance Identification By Assembly

Compute N50/NG50 and auN/auNG

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

Assembling the cause of phenotypes and genotypes from NGS data

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

A package for designing compact and comprehensive capture probe sets.

Fast hash function for DNA sequences

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

Scripts to download genomes from the NCBI FTP servers

Bioinformatics library for .NET

Characterization of Germline variants

🌈Scaffold genome sequence assemblies using linked read sequencing data

SortMeRNA: next-generation sequence filtering and alignment tool

A robust and fast clustering method for amplicon-based studies

A friendly next-generation interface for Genomic data discovery powered by InterMine

A collaboratively written review paper on deep learning, genomics, and precision medicine

MOLGENIS - for scientific data: management, exploration, integration and analysis.

Genome inference from a population reference graph

Parser and database to index the terpene profile of different strains of Cannabis from online databases

UGENE is free open-source cross-platform bioinformatics software

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

LAMBDA – the Local Aligner for Massive Biological DatA

A curated list of awesome Bioinformatics libraries and software.

A tutorial on methods of 16S analysis with QIIME 1

Development repository for the Bioconductor package 'mixOmics '

Simulate genealogical trees and genomic sequence data using population genetic models

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features