595 Open source projects that are alternatives of or similar to dysgu

Complex structural variant detection from WGS data

De novo assembly based variant calling pipeline for Illumina short reads

Toolkit for preparing genomes for submission to NCBI

Rapid large-scale prokaryote pan genome analysis

Ten Quick Tips for Deep Learning in Biology

Antimicrobial Resistance Identification By Assembly

NGLess: NGS with less work

find large indels (in the blind spot between GATK/freebayes and SV callers)

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

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

Official git repository for Biopython (originally converted from CVS)

Haplotype VCF comparison tools

Genomics Extension for SQLite

Bioinformatics library for .NET

A cool place to store your Hi-C

Inference of ploidy and heterozygosity structure using whole genome sequencing data

nim wrapper for htslib for parsing genomics data files

Bayesian haplotype-based mutation calling

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

A tool to circularize genome assemblies

Intuitive local web frontend for the BLAST bioinformatics tool

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

cython + htslib == fast VCF and BCF processing

🔬 BEDOPS: high-performance genomic feature operations

Population-wide Deletion Calling

Fast and accurate gene fusion detection from RNA-Seq data

A faster lmm for GWAS. Supports GPU backend.

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

Bayesian genotyper for structural variants

GCP Essentials for Bioinformatics Researchers

A fast whole-genome aligner based on de Bruijn graphs

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

A collection of scripts and notes related to genomics and bioinformatics

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

An interactive web tool for quality control of DNA sequencing data

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

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

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

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

Reads simulator

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

A powerful open source data warehouse system

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

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

GenomeTools genome analysis system.

An ultrafast memory-efficient short read aligner

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

JavaScript VisualizationTools

A genome browser that shows long reads and complex variants better

simuG: a general-purpose genome simulator

A tool for fast and accurate summarizing of variant calling format (VCF) files

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

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

Model and predict short DNA sequence features with neural networks

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

Deep learning infrastructure for bioinformatics

xHLA: Fast and accurate HLA typing from short read sequence data