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182 search results found

Fastp ⭐ 1,602

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.

Nucleus ⭐ 675

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

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Bwa Mem2 ⭐ 645

The next version of bwa-mem

A high-performance, Pythonic language for bioinformatics

Vsearch ⭐ 605

Versatile open-source tool for microbiome analysis

Bowtie2 ⭐ 594

A fast and sensitive gapped read aligner

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

Ultra-fast and memory-efficient (meta-)genome assembler

Hh Suite ⭐ 429

Remote protein homology detection suite.

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Raxml Ng ⭐ 339

RAxML Next Generation: faster, easier-to-use and more flexible

Structural variant and indel caller for mapped sequencing data

Survivor ⭐ 299

Toolset for SV simulation, comparison and filtering

Octopus ⭐ 285

Bayesian haplotype-based mutation calling

Avogadro ⭐ 283

Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Haplotype VCF comparison tools

🔬 Assemble large genomes using short reads

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

🔬 BEDOPS: high-performance genomic feature operations

Sortmerna ⭐ 220

SortMeRNA: next-generation sequence filtering and alignment tool

Strelka ⭐ 204

Strelka2 germline and somatic small variant caller

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Krakenuniq ⭐ 201

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

UGENE is free open-source cross-platform bioinformatics software

Chromap ⭐ 166

Fast alignment and preprocessing of chromatin profiles

Graphtyper ⭐ 156

Population-scale genotyping using pangenome graphs

Genomicsqlite ⭐ 146

Genomics Extension for SQLite

Cgranges ⭐ 144

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

Poplddecay ⭐ 138

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

SIMD partial order alignment tool/library

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

Rnaseqc ⭐ 132

Fast, efficient RNA-Seq metrics for quality control and process optimization

Foldcomp ⭐ 127

Compressing protein structures effectively with torsion angles

Blacklist ⭐ 121

Application for making ENCODE Blacklists

Strobealign ⭐ 114

Aligns short reads using dynamic seed size with strobemers

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

A robust and fast clustering method for amplicon-based studies

Physicell ⭐ 107

PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!

Kmer Cnt ⭐ 106

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

Gencore ⭐ 103

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

phylogenetics tools for linux (and other mostly posix compliant) computers

Msisensor ⭐ 99

microsatellite instability detection using tumor only or paired tumor-normal data

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Bwa Meme ⭐ 92

BWA-MEME: Faster BWA-MEM2 using learned-index

Snprelate ⭐ 90

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

Gramtools ⭐ 90

Genome inference from a population reference graph

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Tiledb Vcf ⭐ 79

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

A compressed, associative, exact, and weighted dictionary for k-mers.

Fast hash function for DNA/RNA sequences

A fast 23andMe DNA parser and inferrer for Python

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

LAMBDA – the Local Aligner for Massive Biological DatA

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

The software behind Chai's open-source Real-Time PCR instrument

Bonsai: Fast, flexible taxonomic analysis and classification

Pax_sapientica ⭐ 61

🌿: GIS for philological, archaeological, and anthropological data.

Gatb Core ⭐ 61

Core library of the Genome Analysis Toolbox with de-Bruijn graph

Software for predicting library complexity and genome coverage in high-throughput sequencing.

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Substring index for paths in a graph

Metabuli ⭐ 54

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Bayesian MCMC matrix factorization algorithm

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

Cath Tools ⭐ 51

Protein structure comparison tools such as SSAP and SNAP

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Metacache ⭐ 49

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

vcfdist: Accurately benchmarking phased variant calls

A versatile compressor of third generation sequencing reads.

Bioinfortools ⭐ 42

Bioinformatics scripts and tools

Efficient target prediction incorporating accessibility of interaction sites

Seqarray ⭐ 41

Data management of large-scale whole-genome sequence variant calls (Development version only)

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

A fast constructor of the compressed de Bruijn graph from many genomes

A fast tool for hybrid genome assembly of long and short reads

Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop

Fast and Versatile Alignments for Python

Shapeit5 ⭐ 38

Segmented HAPlotype Estimation and Imputation Tool

Megadock ⭐ 38

An ultra-high-performance protein-protein docking for heterogeneous supercomputers

Covtobed ⭐ 36

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

Fast and compact locality-preserving minimal perfect hashing for k-mer sets.

Population-wide Deletion Calling

Classify sequencing reads using MinHash.

Smartpeak ⭐ 30

Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing

Fast & accurate alignment of barcoded short-reads

Mindthegap ⭐ 30

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

GCLib - Genomic C++ library of reusable code for bioinformatics projects

Nonpareil ⭐ 29

Estimate metagenomic coverage and sequence diversity

Fastenloc ⭐ 28

Colocalization analysis of genetic association signals

Rabbittclust ⭐ 28

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

tidy processing of biological sequences in R

Pandoras Toolbox For Bioinformatics ⭐ 26

A collection of well-known bioinformatics programs.

Goldrush ⭐ 26

Linear-time de novo Long Read Assembler

Meshclust ⭐ 25

MeShClust: an intelligent tool for clustering DNA sequences

SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis

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