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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A cool place to store your Hi-C

A fast and sensitive gapped read aligner

A fast 23andMe genome text file parser, now superseded by arv

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

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

Efficient pythonic random access to fasta subsequences

Java utilities for Bioinformatics

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

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

Flexible genotype query among 30,000+ samples whole-genome

A curated list of awesome bioinformatics software.

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.

Earl Grey: A fully automated TE curation and annotation pipeline

A collection of scripts and notes related to genomics and bioinformatics

An open source platform for managing and analyzing biomedical big data

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

annotate a VCF with other VCFs/BEDs/tabixed files

Antimicrobial Resistance Identification By Assembly

Scripts to download genomes from the NCBI FTP servers

A fast whole-genome aligner based on de Bruijn graphs

Python and C++ code for reading and writing genomics data.

GCP Essentials for Bioinformatics Researchers

Analysis pipelines for sequencing data

Genomics Extension for SQLite

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

Fast alignment and preprocessing of chromatin profiles

Predict plasmids from uncorrected long read data

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

De novo assembly based variant calling pipeline for Illumina short reads

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

Example client programs for Saphetor's VarSome annotation API

Assembling the cause of phenotypes and genotypes from NGS data

A high-performance, Pythonic language for bioinformatics

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

A comprehensive tutorial about GWAS and PRS

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

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

NGLess: NGS with less work

Provide R access to the NCI Genomic Data Commons portal.

Tools to process and analyze deep sequencing data.

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

Bayesian genotyper for structural variants

The next version of bwa-mem

Data intensive science for everyone.

Scalable genomic data analysis.

An interactive web tool for quality control of DNA sequencing data

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

Official code repository for GATK versions 4 and up

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Bystro genetic analysis (annotation, filtering, statistics)

An open-access bioinformatics text

A modern genome browser built with JavaScript and HTML5.

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

Model and predict short DNA sequence features with neural networks

Bioinformatics library for .NET