860 Open source projects that are alternatives of or similar to GenomeAnalysisModule

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

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

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

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

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This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Official code repository for GATK versions 4 and up

A fast 23andMe genome text file parser, now superseded by arv

Deep learning infrastructure for bioinformatics

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

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

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

Ten Quick Tips for Deep Learning in Biology

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

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

Intuitive local web frontend for the BLAST bioinformatics tool

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

Predict plasmids from uncorrected long read data

JavaScript VisualizationTools

🔬 Assemble large genomes using short reads

Official git repository for Biopython (originally converted from CVS)

Haplotype VCF comparison tools

Toolkit for preparing genomes for submission to NCBI

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

PERF is an Exhaustive Repeat Finder

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Next generation sequencing reads de novo assembler.

Bayesian haplotype-based mutation calling

Reads simulator

Rapid large-scale prokaryote pan genome analysis

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

nim wrapper for htslib for parsing genomics data files

A powerful open source data warehouse system

Numerical Encoding for Human Genetic Variants

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

Compute N50/NG50 and auN/auNG

🔬 BEDOPS: high-performance genomic feature operations

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

cython + htslib == fast VCF and BCF processing

An ultrafast memory-efficient short read aligner

A faster lmm for GWAS. Supports GPU backend.

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

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

Fast hash function for DNA sequences

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

Provide R access to the NCI Genomic Data Commons portal.

Assembling the cause of phenotypes and genotypes from NGS data

Fast alignment and preprocessing of chromatin profiles

A curated list of awesome bioinformatics software.

An open-access bioinformatics text

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

Bystro genetic analysis (annotation, filtering, statistics)

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

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

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

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

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