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272 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.

Official code repository for GATK versions 4 and up

Cloud-native genomic dataframes and batch computing

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

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

Bowtie2 ⭐ 594

A fast and sensitive gapped read aligner

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

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.

✂️ ⚡ Rapid haploid variant calling and core genome alignment

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

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Bismark ⭐ 335

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

Genome assembly evaluation tool

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

Awesome Cancer Variant Databases ⭐ 284

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

Haplotype VCF comparison tools

Karyoploter ⭐ 278

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

🔬 Assemble large genomes using short reads

Genometools ⭐ 261

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

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

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

Rapid large-scale prokaryote pan genome analysis

Pyfastx ⭐ 211

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

Masurca ⭐ 207

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

UCSC Genome Browser source tree. Stable branch: "beta".

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

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

Ppanggolin ⭐ 191

Build a partitioned pangenome graph from microbial genomes

Insilicoseq ⭐ 158

🚀 A sequencing simulator

Randomly subsample sequencing reads to a specified coverage

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Application and Python module for average nucleotide identity analyses of microbes.

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Sigprofilerextractor ⭐ 132

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

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

Variantspark ⭐ 121

machine learning for genomic variants

Blacklist ⭐ 121

Application for making ENCODE Blacklists

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.

Sigminer ⭐ 119

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/

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

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Pyrodigal ⭐ 111

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Instrain ⭐ 104

Bioinformatics program inStrain

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

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.

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.

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

Genefuse ⭐ 86

Gene fusion detection and visualization

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

A lightweight and high-performance bioinformatics package in Golang

Referenceseeker ⭐ 85

Rapid determination of appropriate reference genomes.

Dotplot large Genomes in an Interactive, Efficient and Simple way

Python graph database framework for bioinformatics

Same species annotation lift over pipeline.

Mining CRISPRs in Environmental Datasets

Tools for processing and analyzing structural variants.

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

Verifybamid ⭐ 78

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

Nucleoatac ⭐ 78

nucleosome calling using ATAC-seq

A fast 23andMe DNA parser and inferrer for Python

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

Python package and CLI for whole-genome duplication related analyses

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.

Pangraph ⭐ 72

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Bonsai: Fast, flexible taxonomic analysis and classification

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

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

Dna Traits ⭐ 64

A fast 23andMe genome text file parser, now superseded by arv

A package for designing compact and comprehensive capture probe sets.

Splitthreader ⭐ 60

Explore rearrangements and copy-number amplifications in a cancer genome

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

Woltka: a versatile meta'omic data classifier

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.

Arioc: GPU-accelerated DNA short-read alignment

⛓ Correct misassemblies using linked AND long reads

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

Long-read splice alignment with high accuracy

Bioinformatics_notes ⭐ 52

Bioinformatics and genomics resources

Metacache ⭐ 49

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

Appliedgenomics2017 ⭐ 49

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

A scalable bacterial genome assembly, annotation and analysis pipeline

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

Deepsomatic ⭐ 45

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

Cloud-based single-cell copy-number variation analysis tool

Mtoolbox ⭐ 44

A bioinformatics pipeline to analyze mtDNA from NGS data

dcHiC: Differential compartment analysis for Hi-C datasets

Snpsplit ⭐ 43

Allele-specific alignment sorting

Phigaro is a scalable command-line tool for predicting phages and prophages

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