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2,080 search results found

Genoverse ⭐ 100

HTML5 scrollable genome browser

SKESA assembler

Pan-genome inference and genotyping with long noisy or short accurate reads

Get_homologues ⭐ 98

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

Phylophlan ⭐ 97

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Large Scale Vrd.pytorch ⭐ 97

Implementation for the AAAI2019 paper "Large-scale Visual Relationship Understanding"

Genomewarp ⭐ 96

GenomeWarp translates genetic variants from one genome assembly version to another.

predicting expression effects of human genome variants ab initio from sequence

Knowledgebase ⭐ 95

recipes that save time

Peregrine ⭐ 94

Peregrine: Fast Genome Assembler Using SHIMMER Index

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

Clonalframeml ⭐ 92

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

A genetic programming engine which evolves solutions through asynchronous speciation.

Sigprofilermatrixgenerator ⭐ 91

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

Bioinformatics ⭐ 90

Code inspired by Bioinformatics Algorithms: an Active Learning Approach.

Osgenome ⭐ 90

An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

mgatk: mitochondrial genome analysis toolkit

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Metamaps ⭐ 88

Long-read metagenomic analysis

A read extraction and realignment tool for next generation sequencing data

Pipeline Structural Variation ⭐ 87

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Hgtector ⭐ 87

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

Finch Rs ⭐ 87

A genomic minhashing implementation in Rust

Hybrid Knowledge Routed Module for Large-scale Object Detection (NerIPS2018)

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

The DNA of Nicholas Cerminara

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

Fast and memory-efficient sequencing error corrector

Genefuse ⭐ 86

Gene fusion detection and visualization

A lightweight and high-performance bioinformatics package in Golang

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

Wholegenomesequencing ⭐ 86

Whole Genome Sequencing analysis, WGS analysis

Referenceseeker ⭐ 85

Rapid determination of appropriate reference genomes.

Dotplot large Genomes in an Interactive, Efficient and Simple way

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

Bacannot ⭐ 85

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Copy number vaiation detection from SNP arrays

Python graph database framework for bioinformatics

Shortstack ⭐ 84

ShortStack: Comprehensive annotation and quantification of small RNA genes

Spliced read mapper for RNA-Seq

Genome Interval Arithmetic in R

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Parliament2 ⭐ 83

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Making whole bacterial genome sequencing data analysis easy

Julia for Whole-genome Analysis Software

Same species annotation lift over pipeline.

Opera Ms ⭐ 82

OPERA-MS - Hybrid Metagenomic Assembler

Sv Cnv Studies ⭐ 81

📚 Relevant papers for CNV and SV approaches

Pb Assembly ⭐ 81

PacBio Assembly Tool Suite: Reads in ⇨ Assembly out

Modular Multi-scale Integrated Genome Graph Browser

Tabula Muris Senis ⭐ 81

Tabula Muris Senis

Ggd Recipes ⭐ 81

conda recipes for genomic data

Human Gem ⭐ 81

The generic genome-scale metabolic model of Homo sapiens

An R package for performing STAAR procedure in whole-genome sequencing studies

Nullarbor ⭐ 80

💾 📃 "Reads to report" for public health and clinical microbiology

Gnomad_methods ⭐ 80

Hail helper functions for the gnomAD project and Translational Genomics Group

Mining CRISPRs in Environmental Datasets

Pytorch Neat ⭐ 80

A pytorch implementation of the NEAT (NeuroEvolution of Augmenting Topologies) algorithm

Mummer2circos ⭐ 79

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Tools for processing and analyzing structural variants.

Nucleoatac ⭐ 78

nucleosome calling using ATAC-seq

Verifybamid ⭐ 78

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

Gwasrapidd ⭐ 78

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data

Hic Data Analysis Bootcamp ⭐ 78

Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Deepsimulator ⭐ 76

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

A fast 23andMe DNA parser and inferrer for Python

MITObim - mitochondrial baiting and iterative mapping

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

Super Mario Neat ⭐ 74

This program evolves an AI using the NEAT algorithm to play Super Mario Bros.

Python package and CLI for whole-genome duplication related analyses

Neuroevolutiondriver ⭐ 74

2D autonomous car navigation with optimal driving lines through NeuroEvolution

A simple RNA-Seq differential gene expression pipeline using Nextflow

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

Telomeric Identifier ⭐ 73

Identify and find telomeres, or telomeric repeats in a genome.

Scrnaseqpipeline ⭐ 73

Ichorcna ⭐ 73

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

An Evolution Simulation Engine written in Objective-C.

Neoantigen Vaccine Pipeline ⭐ 72

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Dnabert_2 ⭐ 72

The official implementation of DNABERT-2.

Rideogram ⭐ 72

Pangraph ⭐ 72

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Ancestry_pipeline ⭐ 71

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

R/qtl: A QTL mapping environment

The Genome Modeling System installer

MOsaic CHromosomal Alterations (MoChA) caller

The GOLang implementation of NeuroEvolution of Augmented Topologies (NEAT) method to evolve and train Artificial Neural Networks without error back propagation

A WGS de novo assembler based on the FMD-index for large genomes

Orthologr ⭐ 68

Genome wide orthology inference and dNdS estimation

Bonsai: Fast, flexible taxonomic analysis and classification

Genome mapping and spliced alignment of cDNA or amino acid sequences

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

Dfast_core ⭐ 67

DDBJ Fast Annotation and Submission Tool

Sars Cov 2 Sequenzdaten_aus_deutschland ⭐ 67

Das Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SARS-CoV-2-Virus bereit. Jedes Labor in Deutschland, das SARS-CoV-2 sequenziert, ist laut der Verordnung zur molekulargenetischen Surveillance des Coronavirus SARS-CoV-2 verpflichtet, dem Robert Koch-Institut die Sequenz- und zugehörige Metadaten zu übermitteln.

Guideseq ⭐ 66

Analysis pipeline for the GUIDE-seq assay.

Bcbio.variation ⭐ 66

Toolkit to analyze genomic variation data, built on the GATK with Clojure

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