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128 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.

Fastp ⭐ 1,602

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

Official code repository for GATK versions 4 and up

Galaxy ⭐ 1,211

Data intensive science for everyone.

C library for high-throughput sequencing data formats

Deeptools ⭐ 644

Tools to process and analyze deep sequencing data.

Jvarkit ⭐ 440

Java utilities for Bioinformatics

Bioconvert ⭐ 344

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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

Tools for working with genomic and high throughput sequencing data.

Sortmerna ⭐ 220

SortMeRNA: next-generation sequence filtering and alignment tool

UGENE is free open-source cross-platform bioinformatics software

R package for analyzing single-cell RNA-seq data

Afterqc ⭐ 157

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

NGLess: NGS with less work

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Mutscan ⭐ 127

Detect and visualize target mutations by scanning FastQ files directly

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

Atropos ⭐ 116

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Gencore ⭐ 103

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

Accurate and flexible loops calling tool for 3D genomic data.

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

🚀 seqfu - Sequece Fastx Utilities

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

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Bwa Meme ⭐ 92

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

Genomics ⭐ 78

Scripts, utilities and programs for genomic bioinformatics.

Callings Nf ⭐ 76

GATK RNA-Seq Variant Calling in Nextflow

A package for designing compact and comprehensive capture probe sets.

Opengene.jl ⭐ 61

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

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.

A scalable bacterial genome assembly, annotation and analysis pipeline

Grabseqs ⭐ 44

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Bamtocov ⭐ 43

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊

Snpsplit ⭐ 43

Allele-specific alignment sorting

Cfdnapattern ⭐ 42

Pattern Recognition for Cell-free DNA

A RepSeq processing swiss-knife

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

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Project metadata manager for PEPs in Python

List of IARC bioinformatics nextflow pipelines

Seqcluster ⭐ 34

small RNA analysis from NGS data

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Read specialized NGS formats as data frames in R, Python, and more.

Bio Dockers ⭐ 32

🐳 Bio-dockers: dockerized bioinformatic tools

Workshop Rnaseq ⭐ 30

Workshop • Analysis of RNA-seq data

A python package and a set of shell commands to handle GTF files

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.

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Csbb Shiny ⭐ 28

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

A (very) fast program for getting statistics about a fastq file, the way I need them, written in Rust

This is the SeqWare Project's main repo.

VAPiD: Viral Annotation and Identification Pipeline

Atacseq_pipeline ⭐ 25

Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.

INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance

Ctdna Pipeline ⭐ 24

A simplified pipeline for ctDNA sequencing data analysis

Ngs Preprocess ⭐ 23

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Fusiondirect.jl ⭐ 23

(No maintenance) Detect gene fusion directly from raw fastq files

Ngstools ⭐ 23

My own tools code for NGS data analysis (Next Generation Sequencing)

Pathogentrack ⭐ 22

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

Haploclique ⭐ 21

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

Project Manager for NGS data analysis

Exon is an OLAP query engine specifically for biology and life science applications.

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Seqmaker.jl ⭐ 19

(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated

A job submitter for Portable Encapsulated Projects

Docker4seq ⭐ 18

Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers.

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Gatk4_best_practice ⭐ 18

GATK4 Best Practice Nextflow Pipeline

Svcollector ⭐ 17

Method to optimally select samples for validation and resequencing

Open_pipelines ⭐ 17

Pipelines for NGS data preprocessing by the Bock lab and friends

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Galaksio ⭐ 17

An easy-to-use way for running Galaxy workflows.

myVCF: a web-based platform for target and exome mutations data management

A Framework to call Structural Variants from NGS based datasets

S4 Clarity Lib ⭐ 16

A modern Python library for BaseSpace Clarity LIMS.

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Covigator Ngs Pipeline ⭐ 15

A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

Pybioviz ⭐ 14

bioinformatics visualization tools with pyviz/bokeh

A robust model for quantitative comparison of ChIP-Seq data sets.

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bioinformatics/btac389

A toolkit for NGS analysis with Python

Rnftools ⭐ 13

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

Grandeur ⭐ 13

UPHL's Reference Free Pipeline

Prophage_tracer ⭐ 13

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

Manuscript describing ChronQC is now available online in Bioinformatics

LAVA: Lightweight Assignment of Variant Alleles

Workshop Ngsintro ⭐ 12

Workshop • Intro to Bioinformatics using NGS data • 5 days

Ngs Handout ⭐ 12

This project is in the process of being ported over to another repository.

Ngs Pipeline ⭐ 12

Pipeline for Somatic Variant Calling with WES and WGS data

Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"

Deepvariant On Spark ⭐ 11

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

Bioinformatics ⭐ 10

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

Sigalign ⭐ 10

A Similarity-Guided Alignment Algorithm

Ngsderive ⭐ 10

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

Artisanal 🤣 bioinformatics tools and pipelines in Scala

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