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504 search results found

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

Deepvariant ⭐ 2,978

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

Minimap2 ⭐ 1,613

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Official code repository for GATK versions 4 and up

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

Galaxy ⭐ 1,211

Data intensive science for everyone.

Getting Started With Genomics Tools And Resources ⭐ 991

Unix, R and python tools for genomics and data science

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Cloud-native genomic dataframes and batch computing

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

Nucleus ⭐ 675

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

Python library to facilitate genome assembly, annotation, and comparative genomics

Bwa Mem2 ⭐ 645

The next version of bwa-mem

Deeptools ⭐ 644

Tools to process and analyze deep sequencing data.

A high-performance, Pythonic language for bioinformatics

Bowtie2 ⭐ 594

A fast and sensitive gapped read aligner

Biojava ⭐ 564

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Pycirclize ⭐ 476

Circular visualization in Python (Circos Plot, Chord Diagram)

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

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

Jvarkit ⭐ 440

Java utilities for Bioinformatics

Jbrowse ⭐ 437

Full-featured and stable genome browser built with JavaScript and HTML5.

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Maftools ⭐ 400

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Minigraph ⭐ 367

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

Arvados ⭐ 354

An open source platform for managing and analyzing biomedical big data

cython + htslib == fast VCF and BCF processing

Postgui ⭐ 335

A React web application to query and share any PostgreSQL database.

Vcfanno ⭐ 334

annotate a VCF with other VCFs/BEDs/tabixed files

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Tools for working with genomic and high throughput sequencing data.

Awesome Bioinformatics Benchmarks ⭐ 290

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

Octopus ⭐ 285

Bayesian haplotype-based mutation calling

Truvari ⭐ 284

Structural variant toolkit for VCFs

Haplotype VCF comparison tools

Canvasxpress ⭐ 282

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Genometools ⭐ 261

GenomeTools genome analysis system.

Sequenceserver ⭐ 259

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A genome browser that shows long reads and complex variants better

🔬 BEDOPS: high-performance genomic feature operations

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

Intermine ⭐ 228

A powerful open source data warehouse system

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

Somalier ⭐ 224

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

Rapid large-scale prokaryote pan genome analysis

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

Deep learning infrastructure for genomics

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

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

Smudgeplot ⭐ 200

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Deep Rules ⭐ 198

Ten Quick Tips for Deep Learning in Biology

Hicexplorer ⭐ 197

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

Miniasm ⭐ 195

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

Circlator ⭐ 193

A tool to circularize genome assemblies

Artemis ⭐ 191

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

Reads simulator

Gwa_tutorial ⭐ 184

A comprehensive tutorial about GWAS and PRS

A cool place to store your Hi-C

Jbrowse Components ⭐ 182

Source code for JBrowse 2, a modern React-based genome browser

Gfatools ⭐ 181

Tools for manipulating sequence graphs in the GFA and rGFA formats

Gcp For Bioinformatics ⭐ 178

GCP for Bioinformatics Researchers

Pygenomeviz ⭐ 177

A genome visualization python package for comparative genomics

Snp Sites ⭐ 173

Finds SNP sites from a multi-FASTA alignment file

Chromap ⭐ 166

Fast alignment and preprocessing of chromatin profiles

Biowasm ⭐ 165

WebAssembly modules for genomics

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Readfish ⭐ 152

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Hts Nim ⭐ 151

nim wrapper for htslib for parsing genomics data files

Gatk Sv ⭐ 148

A structural variation pipeline for short-read sequencing

Genomicsqlite ⭐ 146

Genomics Extension for SQLite

Bio Playground ⭐ 146

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

Cgranges ⭐ 144

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

NGLess: NGS with less work

Antimicrobial Resistance Identification By Assembly

Computationalgenomicsmanual ⭐ 135

Robs manual for the computational genomics and bioinformatics class.

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Gubbins ⭐ 133

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

Population-scale genomics

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

Assemblytics ⭐ 124

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Genome_updater ⭐ 123

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Dnanalyzer ⭐ 122

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Blacklist ⭐ 121

Application for making ENCODE Blacklists

Redundans ⭐ 121

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Chewbbaca ⭐ 113

BSR-Based Allele Calling Algorithm

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

Kmer Cnt ⭐ 106

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

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Open Cravat ⭐ 98

A modular annotation tool for genomic variants

Bioinformatics library for .NET

🚀 seqfu - Sequece Fastx Utilities

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

Ga4gh Server ⭐ 95

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Related Searches

Python Bioinformatics (1,492)

R Bioinformatics (517)

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Genome Genomics (297)

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