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2,082 search results found

Deepvariant ⭐ 2,978

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

Iamdinosaur ⭐ 2,760

🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus

RNA-seq aligner

Official code repository for GATK versions 4 and up

Nextstrain build for novel coronavirus SARS-CoV-2

Ai Programmer ⭐ 1,073

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

tools for working with genome variation graphs

Bottom Up Attention ⭐ 979

Bottom-up attention model for image captioning and VQA, based on Faster R-CNN and Visual Genome

Cloud-native genomic dataframes and batch computing

Applied Computational Genomics ⭐ 887

Applied Computational Genomics Course at UU: Spring 2020

Bedtools2 ⭐ 876

bedtools - the swiss army knife for genome arithmetic

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

Awesome Genome Visualization ⭐ 663

A list of interesting genome browser or genome-browser-like implementations

Pygenometracks ⭐ 654

python module to plot beautiful and highly customizable genome browser tracks

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

Mosdepth ⭐ 617

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

A single molecule sequence assembler for genomes large and small.

Bowtie2 ⭐ 594

A fast and sensitive gapped read aligner

Ban Vqa ⭐ 527

Bilinear attention networks for visual question answering

Biotools ⭐ 525

A list of useful bioinformatics resources

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

Dnabert ⭐ 471

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Samplot ⭐ 458

Plot structural variant signals from many BAMs and CRAMs

Hic_tools ⭐ 454

A collection of tools for Hi-C data analysis

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

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

Jbrowse ⭐ 437

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

Awesome Crispr ⭐ 431

List of software/websites/databases/other stuff for genome engineering

Unicycler ⭐ 428

hybrid assembly pipeline for bacterial genomes

⚡ ♒ Rapid prokaryotic genome annotation

Vcftools ⭐ 415

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Pytorch Neat ⭐ 387

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Represent Map ⭐ 360

Visualize your startup community on a custom Google map. Based on the code for http://represent.la

Snakepipes ⭐ 359

Customizable workflows based on snakemake and python for the analysis of NGS data

Dna2json ⭐ 357

Formats your genome file as JSON

Genomepy ⭐ 355

genes and genomes at your fingertips

Graph-based alignment (Hierarchical Graph FM index)

Liftoff ⭐ 335

An accurate GFF3/GTF lift over pipeline

Bismark ⭐ 335

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

Visual_genome_python_driver ⭐ 328

A python wrapper for the Visual Genome API

Genome assembly evaluation tool

Na12878 ⭐ 321

Data and analysis for NA12878 genome on nanopore

Metawrap ⭐ 320

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

the pangenome graph builder

Fastani ⭐ 301

Fast Whole-Genome Similarity (ANI) Estimation

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

Extensive de-novo TE Annotator

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Atac Seq Pipeline ⭐ 290

ENCODE ATAC-seq pipeline

Multineat ⭐ 289

Portable NeuroEvolution Library

Tools for fast and flexible genome assembly scaffolding and improvement

Awesome Cancer Variant Databases ⭐ 284

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Haplotype VCF comparison tools

Bactopia ⭐ 281

A flexible pipeline for complete analysis of bacterial genomes

Karyoploter ⭐ 278

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Pycircos ⭐ 277

🔬 Assemble large genomes using short reads

a lightweight db framework for exploring genetic variation.

Synteny and Rearrangement Identifier

Ideogram ⭐ 265

Chromosome visualization for the web

Trycycler ⭐ 264

A tool for generating consensus long-read assemblies for bacterial genomes

NCBI Prokaryotic Genome Annotation Pipeline

Funannotate ⭐ 261

Eukaryotic Genome Annotation Pipeline

Genometools ⭐ 261

GenomeTools genome analysis system.

Datasets ⭐ 259

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Celloracle ⭐ 253

This is the alpha version of the CellOracle package

A genome browser that shows long reads and complex variants better

the original fractal flame renderer and genetic language

Mashmap ⭐ 243

A fast approximate aligner for long DNA sequences

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

Read coverage calculator for metagenomics

Augustus ⭐ 237

Genome annotation with AUGUSTUS

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Personal Cancer Genome Reporter (PCGR)

Merqury ⭐ 234

k-mer based assembly evaluation

Crispresso2 ⭐ 233

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

Ngsplot ⭐ 231

Quick mining and visualization of NGS data by integrating genomic databases

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

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

Rapid large-scale prokaryote pan genome analysis

PEPPER-Margin-DeepVariant

Genome-wide Efficient Mixed Model Association

Centrifuge ⭐ 215

Classifier for metagenomic sequences

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Getorganelle ⭐ 209

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

Dalliance ⭐ 208

Interactive web-based genome browser.

Masurca ⭐ 207

Interval data structure

Chromosomemappings ⭐ 204

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

Krakenuniq ⭐ 201

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

Smudgeplot ⭐ 200

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Rapid comparison and dereplication of genomes

Biomartr ⭐ 198

Genomic Data Retrieval with R

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