Cargando…

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

BACKGROUND: Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenom...

Descripción completa

Detalles Bibliográficos
Autores principales:	Clarke, Erik L., Taylor, Louis J., Zhao, Chunyu, Connell, Andrew, Lee, Jung-Jin, Fett, Bryton, Bushman, Frederic D., Bittinger, Kyle
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2019
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429786/ https://www.ncbi.nlm.nih.gov/pubmed/30902113 http://dx.doi.org/10.1186/s40168-019-0658-x

Ejemplares similares

The SC has a sunbeam
Publicado: (1978)

UMGAP: the Unipept MetaGenomics Analysis Pipeline
por: Van der Jeugt, Felix, et al.
Publicado: (2022)

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
por: Uritskiy, Gherman V., et al.
Publicado: (2018)

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
por: Ferravante, Carlo, et al.
Publicado: (2021)

The SunBEAm birth cohort: Protocol design
por: Keet, Corinne, et al.
Publicado: (2023)

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
por: Kim, Jiwoong, et al.
Publicado: (2016)

A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank
por: Abebe, Michael, et al.
Publicado: (2013)

ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently
por: Tian, Renmao, et al.
Publicado: (2022)

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
por: Lai, Binbin, et al.
Publicado: (2015)

ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies
por: Plyusnin, Ilya, et al.
Publicado: (2022)

Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons
por: Zaidi, Syed Shujaat Ali, et al.
Publicado: (2021)

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
por: Treangen, Todd J, et al.
Publicado: (2013)

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
por: Narayanasamy, Shaman, et al.
Publicado: (2016)

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
por: Kushwaha, Sandeep K, et al.
Publicado: (2015)

ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data
por: Wylie, Todd N., et al.
Publicado: (2021)

MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline
por: Eng, Alexander, et al.
Publicado: (2020)

ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data
por: Vetter, Julia, et al.
Publicado: (2022)

DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies
por: Faure, Andre J., et al.
Publicado: (2020)

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
por: Kalari, Krishna R, et al.
Publicado: (2014)

BS-Seeker3: ultrafast pipeline for bisulfite sequencing
por: Huang, Kevin Yu Yuan, et al.
Publicado: (2018)

ESTPiper – a web-based analysis pipeline for expressed sequence tags
por: Tang, Zuojian, et al.
Publicado: (2009)

An integrated computational pipeline and database to support whole-genome sequence annotation
por: Mungall, CJ, et al.
Publicado: (2002)

A software pipeline for processing and identification of fungal ITS sequences
por: Nilsson, R Henrik, et al.
Publicado: (2009)

Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations
por: Lee, Aaron Y., et al.
Publicado: (2016)

MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment
por: Sun, Shuying, et al.
Publicado: (2013)

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
por: Guo, Weilong, et al.
Publicado: (2013)

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data
por: Christley, Scott, et al.
Publicado: (2017)

TAMA: improved metagenomic sequence classification through meta-analysis
por: Sim, Mikang, et al.
Publicado: (2020)

A big data approach to metagenomics for all-food-sequencing
por: Kobus, Robin, et al.
Publicado: (2020)

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data
por: de Nies, Laura, et al.
Publicado: (2021)

InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data
por: Xiong, Wenwei, et al.
Publicado: (2013)

Kismeth: Analyzer of plant methylation states through bisulfite sequencing
por: Gruntman, Eyal, et al.
Publicado: (2008)

MAP MUTATION: a program for analyzing mutations in protein sequences
por: Anwar, Tamanna, et al.
Publicado: (2006)

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data
por: Sun, Zhifu, et al.
Publicado: (2014)

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
por: Wolfien, Markus, et al.
Publicado: (2016)

TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences
por: Hung, Sheng-Jou, et al.
Publicado: (2016)

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
por: Wöste, Marius, et al.
Publicado: (2020)

msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data
por: Kim, Heesun, et al.
Publicado: (2022)

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
por: Eagles, Nicholas J., et al.
Publicado: (2023)

A-GAME: improving the assembly of pooled functional metagenomics sequence data
por: Chiara, Matteo, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_inkkvt05ja0pqpttnqqha9ucig