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108 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

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.

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.

Truvari ⭐ 284

Structural variant toolkit for VCFs

A Java API for high-throughput sequencing data (HTS) formats.

Sequenceserver ⭐ 259

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

Comp Genomics Class ⭐ 236

Code and examples for JHU Computational Genomics class

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

Rapid large-scale prokaryote pan genome analysis

Miso Lims ⭐ 214

MISO: An open-source LIMS for NGS sequencing centres

Smudgeplot ⭐ 200

Inference of ploidy and heterozygosity structure using whole genome 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

Reads simulator

Snp Sites ⭐ 173

Finds SNP sites from a multi-FASTA alignment file

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

Genomicsqlite ⭐ 146

Genomics Extension for SQLite

Antimicrobial Resistance Identification By Assembly

Gubbins ⭐ 133

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

Identification of differential RNA modifications from nanopore direct RNA sequencing

Dnanalyzer ⭐ 122

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

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

🚀 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

Wally: Visualization of aligned sequencing reads and contigs

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

A package for designing compact and comprehensive capture probe sets.

xHLA: Fast and accurate HLA typing from short read sequence data

Bioinformatics_notes ⭐ 52

Bioinformatics and genomics resources

Appliedgenomics2017 ⭐ 49

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

Chanjo provides a better way to analyze coverage data in clinical sequencing.

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.

A versatile compressor of third generation sequencing reads.

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

10x Genomics Reads Simulator

Pathogen Informatics Training ⭐ 38

de novo virus assembler of Illumina paired reads

Tools for analyzing 10X Genomics data

Biocommons.seqrepo ⭐ 34

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

Position-wise analysis of sequencing and genomics data

Bio Dockers ⭐ 32

🐳 Bio-dockers: dockerized bioinformatic tools

Course materials for the edX Data Analysis for Genomics

Wochenende ⭐ 30

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

The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Wiggleplotr ⭐ 28

A small R package to make sequencing read coverage plots in R.

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Deepstats ⭐ 27

deepStats: a stastitical toolbox for deeptools and genomic signals

Awesome Sequencing Tech Papers ⭐ 26

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

Smallrnaseq ⭐ 26

small rna-seq analysis package

Teaching ⭐ 25

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

Gff3toembl ⭐ 20

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Sequenceng ⭐ 18

An interactive learning resource for next-generation sequencing (NGS) techniques

Course Materials for Genomics Data Mining

Tools for producing pseudo-cgh of next-generation sequencing data

Ctdnatools ⭐ 17

R package to work with ctDNA sequencing data

Appliedgenomics2019 ⭐ 16

Materials for Spring 2019 Applied Genomics Course

Java Genomics Toolkit ⭐ 16

Collection of scripts for working with Wiggle files and analyzing sequencing data

Bioutils ⭐ 16

provides common tools and lookup tables used primarily by the hgvs and uta packages

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

Bio Tradis ⭐ 15

A set of tools to analyse the output from TraDIS analyses

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

A straightforward and complete next-generation sequencing read simulator

Dtc_scripts ⭐ 14

Scripts to Analyze DTC Sequencing and Genotyping Data (and some comparisons to Veritas WGS data)

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

Saffrontree ⭐ 14

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Nanorepeat ⭐ 13

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

Prophage_tracer ⭐ 13

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

Microsatellite Instability Classification using Multiple Instance Learning

Assigner ⭐ 12

Population assignment analysis using R

Scisa Tools ⭐ 12

single-cell-Isoform-Sequencing-Analysis-Tools: New and powerful tools brings single-cell RNA sequencing to the Isoform level and single molecule resolution.

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling fr

1000 Genomes Project Metadata R Package

Hcov 19 Genomics ⭐ 12

SARS-CoV-2 genomics

[in development] Proof-of-Concept variation translation, validation, and registration service

Lodestone ⭐ 11

Mycobacterial pipeline

Deepvariant On Spark ⭐ 11

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

Ngsderive ⭐ 10

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

Banzai Microbialgenomics Pipeline ⭐ 10

Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool developed within Dr Scott Beatson’s Group at the University of Queensland

Readdatastores.jl ⭐ 10

Datastores for reads, not your papa's FASTQ files.

Haplotype phaser for next-generation sequencing data

Screclassify ⭐ 8

Post hoc cell type classification of single-cell RNA-sequencing data.

Ruby Htslib ⭐ 7

HTSlib bindings for Ruby

Fastq.bio Serverless ⭐ 7

An interactive web tool for quality control of DNA sequencing data, using Cloudflare workers running WebAssembly

Albatradis ⭐ 7

Comparative TraDIS analysis

Cg Pipeline ⭐ 6

Genome assembly/prediction/annotation pipeline for the Linux command line

Filters for Next Generation Sequencing

Appliedgenomeresearch ⭐ 6

course about NGS data processing: genomics and transcriptomics

Pyminknow ⭐ 6

Mock minKNOW gRPC server

[source] CELLO - Cancer EvoLution toolbox for LOngitudinal data

Deep Learning For Genomics ⭐ 5

Using deep learning methods on single-cell sequencing data for classification of cell types

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