578 Open source projects that are alternatives of or similar to unimap

Official git repository for Biopython (originally converted from CVS)

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

Bayesian genotyper for structural variants

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

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

An interactive web tool for quality control of DNA sequencing data

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

A cool place to store your Hi-C

A genome browser that shows long reads and complex variants better

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

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

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

Official code repository for GATK versions 4 and up

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

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

Antimicrobial Resistance Identification By Assembly

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A tool to circularize genome assemblies

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

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

Deep learning infrastructure for bioinformatics

Rapid large-scale prokaryote pan genome analysis

An ultrafast memory-efficient short read aligner

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

cython + htslib == fast VCF and BCF processing

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A collection of publications on comparison of high-throughput sequencing technologies.

Analysis pipelines for sequencing data

Efficient variant-call data storage and retrieval library using the TileDB storage library.

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

Model and predict short DNA sequence features with neural networks

A fast whole-genome aligner based on de Bruijn graphs

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

A collection of scripts and notes related to genomics and bioinformatics

Genomics Extension for SQLite

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

NGLess: NGS with less work

Toolkit for preparing genomes for submission to NCBI

Data intensive science for everyone.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Bayesian haplotype-based mutation calling

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

nim wrapper for htslib for parsing genomics data files

Ten Quick Tips for Deep Learning in Biology

Reads simulator

GenomeTools genome analysis system.

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

🔬 BEDOPS: high-performance genomic feature operations

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

Intuitive local web frontend for the BLAST bioinformatics tool

Haplotype VCF comparison tools

Python and C++ code for reading and writing genomics data.

Scalable genomic data analysis.

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

A powerful open source data warehouse system

JavaScript VisualizationTools

A faster lmm for GWAS. Supports GPU backend.