614 Open source projects that are alternatives of or similar to Jbrowse

An open-access bioinformatics text

Java utilities for Bioinformatics

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

Ten Quick Tips for Deep Learning in Biology

A powerful open source data warehouse system

Scripts to download genomes from the NCBI FTP servers

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Example client programs for Saphetor's VarSome annotation API

Haplotype VCF comparison tools

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

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

🔬 BEDOPS: high-performance genomic feature operations

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

JavaScript VisualizationTools

An ultrafast memory-efficient short read aligner

An open source platform for managing and analyzing biomedical big data

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

A faster lmm for GWAS. Supports GPU backend.

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

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

A package for designing compact and comprehensive capture probe sets.

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

Provide R access to the NCI Genomic Data Commons portal.

Assembling the cause of phenotypes and genotypes from NGS data

A high-performance, Pythonic language for bioinformatics

DOM Text Based Multiple Sequence Alignment Library

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

Intuitive local web frontend for the BLAST bioinformatics tool

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

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

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

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

Official git repository for Biopython (originally converted from CVS)

cython + htslib == fast VCF and BCF processing

Predict AMPs in (meta)genomes and peptides

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

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

Toolkit for preparing genomes for submission to NCBI

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

Fast hash function for DNA sequences

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

Compute N50/NG50 and auN/auNG

GenomeTools genome analysis system.

Feature Annotation Location Description Ontology

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Bystro genetic analysis (annotation, filtering, statistics)

annotate a VCF with other VCFs/BEDs/tabixed files

Fast alignment and preprocessing of chromatin profiles

Efficient pythonic random access to fasta subsequences

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

Earl Grey: A fully automated TE curation and annotation pipeline

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

Predict plasmids from uncorrected long read data

A comprehensive tutorial about GWAS and PRS

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

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.

Deep learning infrastructure for bioinformatics

A genome browser that shows long reads and complex variants better

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

A curated list of awesome bioinformatics software.