1083 Open source projects that are alternatives of or similar to wdlRunR

Provide R access to the NCI Genomic Data Commons portal.

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

A faster lmm for GWAS. Supports GPU backend.

Bayesian haplotype-based mutation calling

An interactive web tool for quality control of DNA sequencing data

Genomics Extension for SQLite

NGLess: NGS with less work

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

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

Deep learning infrastructure for bioinformatics

Intuitive local web frontend for the BLAST bioinformatics tool

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

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

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

A fast whole-genome aligner based on de Bruijn graphs

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

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

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

GCP Essentials for Bioinformatics Researchers

Rapid large-scale prokaryote pan genome analysis

Reads simulator

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

A genome browser that shows long reads and complex variants better

cython + htslib == fast VCF and BCF processing

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

JavaScript VisualizationTools

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

Model and predict short DNA sequence features with neural networks

Toolkit for preparing genomes for submission to NCBI

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

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

Bayesian genotyper for structural variants

Bioinformatics library for .NET

Analysis pipelines for sequencing data

A collection of scripts and notes related to genomics and bioinformatics

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A cool place to store your Hi-C

Antimicrobial Resistance Identification By Assembly

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

A tool to circularize genome assemblies

nim wrapper for htslib for parsing genomics data files

Lightweight Iterative Gene set Enrichment in R

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

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

Ten Quick Tips for Deep Learning in Biology

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

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

GenomeTools genome analysis system.

A powerful open source data warehouse system

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

An ultrafast memory-efficient short read aligner

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

Official git repository for Biopython (originally converted from CVS)

🔬 BEDOPS: high-performance genomic feature operations

Bioconductor package for management of multi-assay data

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

Official code repository for GATK versions 4 and up

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Haplotype VCF comparison tools