579 Open source projects that are alternatives of or similar to EarlGrey

Toolkit for preparing genomes for submission to NCBI

Example client programs for Saphetor's VarSome annotation API

Fast alignment and preprocessing of chromatin profiles

A fast 23andMe genome text file parser, now superseded by arv

Provide R access to the NCI Genomic Data Commons portal.

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

Intuitive local web frontend for the BLAST bioinformatics tool

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

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

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Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

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

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

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

An ultrafast memory-efficient short read aligner

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LRSDAY: Long-read Sequencing Data Analysis for Yeasts

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

An open-access bioinformatics text

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

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

A package for designing compact and comprehensive capture probe sets.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Bayesian haplotype-based mutation calling

nim wrapper for htslib for parsing genomics data files

Genotyping of segregating mobile elements insertions

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

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

A curated list of bioinformatics bench-marking papers and resources.

Reads simulator

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

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

A powerful open source data warehouse system

Deep learning infrastructure for bioinformatics

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

🔬 BEDOPS: high-performance genomic feature operations

Assembling the cause of phenotypes and genotypes from NGS data

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

Genome Annotation Without Nightmares

Haplotype VCF comparison tools

Extensive de-novo TE Annotator

JavaScript VisualizationTools

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

A faster lmm for GWAS. Supports GPU backend.

Official git repository for Biopython (originally converted from CVS)

Fast hash function for DNA sequences

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

Compute N50/NG50 and auN/auNG

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

Bystro genetic analysis (annotation, filtering, statistics)

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

A tool to circularize genome assemblies

cython + htslib == fast VCF and BCF processing

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

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