Haplotype VCF comparison tools
Official git repository for Biopython (originally converted from CVS)
cython + htslib == fast VCF and BCF processing
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
An ultrafast memory-efficient short read aligner
A Java API for high-throughput sequencing data (HTS) formats.
Performant Pythonic GenomicRanges
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
🔬 BEDOPS: high-performance genomic feature operations
SDK for GPU accelerated genome assembly and analysis
Fast large scale matrix visualization for the web.
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Proof-of-concept seq-to-graph mapper and graph generator
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Intuitive local web frontend for the BLAST bioinformatics tool
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.
A genome browser that shows long reads and complex variants better
Chromosome visualization for the web
Deep learning infrastructure for bioinformatics
Ten Quick Tips for Deep Learning in Biology
Rapid large-scale prokaryote pan genome analysis
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
An open-source toolkit for large-scale genomic analysis
Tools to work with variant call format files
structural variant calling and genotyping with existing tools, but, smoothly.
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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
Bayesian haplotype-based mutation calling
nim wrapper for htslib for parsing genomics data files
MISO: An open-source LIMS for NGS sequencing centres
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
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
Code examples of fast and simple k-mer counters for tutorial purposes
A tool to circularize genome assemblies
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
NGLess: NGS with less work
An R package for creating Q-Q and manhattan plots from GWAS results
A cool place to store your Hi-C
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
variant expressions, annotation, and filtering for great good.
Simulate genealogical trees and genomic sequence data using population genetic models
A collection of scripts and notes related to genomics and bioinformatics
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Antimicrobial Resistance Identification By Assembly
Bioinformatics library for .NET
Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features