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169 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.

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.

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

Cutadapt ⭐ 475

Cutadapt removes adapter sequences from sequencing reads

Structural variant and indel caller for mapped sequencing data

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.

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

Truvari ⭐ 284

Structural variant toolkit for VCFs

Sequenceserver ⭐ 259

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

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

Sortmerna ⭐ 220

SortMeRNA: next-generation sequence filtering and alignment tool

Rapid large-scale prokaryote pan genome analysis

Serratus ⭐ 219

Ultra-deep search for novel viruses

Smudgeplot ⭐ 200

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

Splatter ⭐ 195

Simple simulation of single-cell RNA sequencing data

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

UGENE is free open-source cross-platform bioinformatics software

Reads simulator

Snp Sites ⭐ 173

Finds SNP sites from a multi-FASTA alignment file

Insilicoseq ⭐ 158

🚀 A sequencing simulator

Afterqc ⭐ 157

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

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

Awesome Vdj ⭐ 150

📚 Tools and databases for analyzing HLA and VDJ genes.

Genomicsqlite ⭐ 146

Genomics Extension for SQLite

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Antimicrobial Resistance Identification By Assembly

Gubbins ⭐ 133

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

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

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.

Dnanalyzer ⭐ 122

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

Dragonstar2019 ⭐ 122

Decontam ⭐ 122

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

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

Rnalysis ⭐ 114

RNA sequencing analysis software

Vdjtools ⭐ 113

Post-analysis of immune repertoire sequencing data

Bam Error Stats Tool (best): analysis of error types in aligned reads.

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

Gencore ⭐ 103

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

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

Msisensor ⭐ 99

microsatellite instability detection using tumor only or paired tumor-normal data

🚀 seqfu - Sequece Fastx Utilities

Fastq.bio ⭐ 93

An interactive web tool for quality control of DNA sequencing data

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

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.

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

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

Compacted and colored de Bruijn graph construction and querying

Software for predicting library complexity and genome coverage in high-throughput sequencing.

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.

Nanocompore ⭐ 56

RNA modifications detection from Nanopore dRNA-Seq data

Qiime16stutorial ⭐ 55

A tutorial on methods of 16S analysis with QIIME 1

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

Bioinformatics_notes ⭐ 52

Bioinformatics and genomics resources

Appliedgenomics2017 ⭐ 49

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

Python3 scripts to manipulate FASTA and FASTQ files

Deepsomatic ⭐ 45

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

Grabseqs ⭐ 44

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

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

Fluentdna ⭐ 43

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

A versatile compressor of third generation sequencing reads.

Snpsplit ⭐ 43

Allele-specific alignment sorting

Viral infection diagnostics using next-generation sequencing

Hic_pipeline ⭐ 40

An easy-to-use Hi-C data processing software supporting distributed computation.

A RepSeq processing swiss-knife

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

A fast tool for hybrid genome assembly of long and short reads

Shapeit5 ⭐ 38

Segmented HAPlotype Estimation and Imputation Tool

SARS-CoV-2 workflow for nanopore sequence data

Galaxy Rna Workbench ⭐ 38

Galaxy RNA workbench

Pathogen Informatics Training ⭐ 38

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

10x Genomics Reads Simulator

de novo virus assembler of Illumina paired reads

Wisecondorx ⭐ 35

WisecondorX — An evolved WISECONDOR

Seqcluster ⭐ 34

small RNA analysis from NGS data

Biocommons.seqrepo ⭐ 34

non-redundant, compressed, journalled, file-based storage for biological sequences

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

Bio Dockers ⭐ 32

🐳 Bio-dockers: dockerized bioinformatic tools

Covid 19 Signal ⭐ 32

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Lordfast ⭐ 31

Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

Next-Gen Sequencing tools from the Horvath Lab

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Smallrnaseq ⭐ 26

small rna-seq analysis package

Awesome Sequencing Tech Papers ⭐ 26

A collection of publications on comparison of high-throughput sequencing technologies.

Pipeliner ⭐ 25

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Ctdna Pipeline ⭐ 24

A simplified pipeline for ctDNA sequencing data analysis

Informatics On High Throughput Sequencing Data Course Summer 2020 ⭐ 24

This is a summer training course at CCIC (Faculty of Computers and Information), Mansoura University, Egypt.

Bioinformatics Course 2020 ⭐ 23

Ngstools ⭐ 23

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

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