Topic: ngs Goto Github
Some thing interesting about ngs
Some thing interesting about ngs
ngs,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
Organization: 3dgenomes
ngs,Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Organization: ablab
Home Page: https://ablab.github.io/IsoQuant/
ngs,A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Organization: aidenlab
Home Page: http://aidenlab.org
ngs,Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Organization: bioconvert
Home Page: http://bioconvert.readthedocs.io
ngs,A method for variant graph genotyping based on exact alignment of k-mers
Organization: bioinformatics-centre
ngs,Official code repository for GATK versions 4 and up
Organization: broadinstitute
Home Page: https://software.broadinstitute.org/gatk
ngs,V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Organization: cbg-ethz
Home Page: https://cbg-ethz.github.io/V-pipe/
ngs,Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Organization: costalab
Home Page: https://reg-gen.readthedocs.io/
ngs,GATK RNA-Seq Variant Calling in Nextflow
Organization: crg-cnag
ngs,Cloud agnostic genomics analysis, scientific computation and storage platform
Organization: epam
Home Page: https://cloud-pipeline.com
ngs,A collection of awesome things regarding all omics.
User: flowhub-team
ngs,Tools for working with genomic and high throughput sequencing data.
Organization: fulcrumgenomics
Home Page: http://fulcrumgenomics.github.io/fgbio/
ngs,Data intensive science for everyone.
Organization: galaxyproject
Home Page: https://galaxyproject.org
ngs,A collection of Galaxy-related training material
Organization: galaxyproject
Home Page: https://training.galaxyproject.org
ngs,DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Organization: google
ngs,Publication quality NGS track plotting
User: harbourlab
ngs,R package for analyzing single-cell RNA-seq data
Organization: hms-dbmi
Home Page: http://pklab.med.harvard.edu/scde
ngs,Pathogen NGS Documentary
User: indexofire
Home Page: https://indexofire.github.io/pathongs
ngs,Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
User: jodyphelan
ngs,BWA-MEME: Faster BWA-MEM2 using learned-index
Organization: kaist-ina
Home Page: https://ina.kaist.ac.kr/projects/bwa-meme/
ngs,Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
Organization: khp-informatics
ngs,Recentrifuge: robust comparative analysis and contamination removal for metagenomics
User: khyox
Home Page: http://www.recentrifuge.org
ngs,Annotation and Ranking of Structural Variation
User: lgmgeo
ngs,Java utilities for Bioinformatics
User: lindenb
Home Page: https://jvarkit.readthedocs.io/
ngs,A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
User: louiejtaylor
ngs,Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
User: lucapinello
ngs,Customizable workflows based on snakemake and python for the analysis of NGS data
Organization: maxplanck-ie
Home Page: http://snakepipes.readthedocs.io
ngs,NGLess: NGS with less work
Organization: ngless-toolkit
Home Page: https://ngless.embl.de
ngs,A cool place to store your Hi-C
Organization: open2c
Home Page: https://open2c.github.io/cooler
ngs,Extract 3D contacts (.pairs) from sequencing alignments
Organization: open2c
ngs,Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Organization: opengene
ngs,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.
Organization: opengene
ngs,Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
Organization: opengene
ngs,Detect and visualize target mutations by scanning FastQ files directly
Organization: opengene
ngs,Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
User: oschwengers
Home Page: https://doi.org/10.1099/mgen.0.000398
ngs,HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
User: seppinho
Home Page: https://haplogrep.i-med.ac.at/
ngs,SortMeRNA: next-generation sequence filtering and alignment tool
Organization: sortmerna
Home Page: https://sortmerna.readthedocs.io
ngs,:rocket: seqfu - Sequece Fastx Utilities
User: telatin
Home Page: https://telatin.github.io/seqfu2
ngs,UGENE is free open-source cross-platform bioinformatics software
Organization: ugeneunipro
Home Page: http://ugene.net
ngs,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.
Organization: vanheeringen-lab
Home Page: https://vanheeringen-lab.github.io/seq2science
ngs,Accurate and flexible loops calling tool for 3D genomic data.
User: yaqiangcao
Home Page: https://yaqiangcao.github.io/cLoops/
ngs,Rare variant test software for next generation sequencing data
User: zhanxw
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