Cargando…

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes

BACKGROUND: High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelines are needed to analyze and compare these genomes. Although several approaches...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ruiz-Perez, Carlos A., Conrad, Roth E., Konstantinidis, Konstantinos T.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2021
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7789693/ https://www.ncbi.nlm.nih.gov/pubmed/33407081 http://dx.doi.org/10.1186/s12859-020-03940-5

Ejemplares similares

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
por: Chen, I-Min A., et al.
Publicado: (2016)

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes
por: Estill, James C, et al.
Publicado: (2009)

UTAP: User-friendly Transcriptome Analysis Pipeline
por: Kohen, Refael, et al.
Publicado: (2019)

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

LotuS: an efficient and user-friendly OTU processing pipeline
por: Hildebrand, Falk, et al.
Publicado: (2014)

SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files
por: Bai, Yongsheng
Publicado: (2014)

Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes
por: Lueder, Matthew R., et al.
Publicado: (2021)

Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data
por: Cullen, Jonah N, et al.
Publicado: (2023)

ArrayIDer: automated structural re-annotation pipeline for DNA microarrays
por: van den Berg, Bart HJ, et al.
Publicado: (2009)

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
por: Holt, Carson, et al.
Publicado: (2011)

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations
por: Yang, Yongzhi, et al.
Publicado: (2019)

Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences
por: Yu, Xiaoyu
Publicado: (2023)

CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes
por: Vassilieff, Héléna, et al.
Publicado: (2022)

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

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
por: Fallon, Timothy R., et al.
Publicado: (2023)

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
por: Kumar, Surendra, et al.
Publicado: (2011)

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites
por: Spinozzi, Giulio, et al.
Publicado: (2017)

The Genome Reverse Compiler: an explorative annotation tool
por: Warren, Andrew S, et al.
Publicado: (2009)

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

annot8r: GO, EC and KEGG annotation of EST datasets
por: Schmid, Ralf, et al.
Publicado: (2008)

Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data
por: Gao, Jianing, et al.
Publicado: (2017)

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
por: Kondratenko, Yulia, et al.
Publicado: (2020)

Mining locus tags in PubMed Central to improve microbial gene annotation
por: Stubben, Chris J, et al.
Publicado: (2014)

Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome
por: Tcherepanov, Vasily, et al.
Publicado: (2006)

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes
por: Tchechmedjiev, Andon, et al.
Publicado: (2018)

GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data
por: Sessa, Emily B., et al.
Publicado: (2023)

Genepi: a blackboard framework for genome annotation
por: Descorps-Declère, Stéphane, et al.
Publicado: (2006)

VIGOR, an annotation program for small viral genomes
por: Wang, Shiliang, et al.
Publicado: (2010)

AnnotateGenomicRegions: a web application
por: Zammataro, Luca, et al.
Publicado: (2014)

Dintor: functional annotation of genomic and proteomic data
por: Weichenberger, Christian X., et al.
Publicado: (2015)

VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
por: Shean, Ryan C., et al.
Publicado: (2019)

Variation ontology: annotator guide
por: Vihinen, Mauno
Publicado: (2014)

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer
por: Abate, Francesco, et al.
Publicado: (2014)

SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation
por: Salz, Renee, et al.
Publicado: (2023)

Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants
por: Shih, Ching-Yu, et al.
Publicado: (2021)

Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation.
por: de Almeida, Felipe Marques, et al.
Publicado: (2023)

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease
por: Sifrim, Alejandro, et al.
Publicado: (2012)

AnnoTrack - a tracking system for genome annotation
por: Kokocinski, Felix, et al.
Publicado: (2010)

Eval: A software package for analysis of genome annotations
por: Keibler, Evan, et al.
Publicado: (2003)

BEACON: automated tool for Bacterial GEnome Annotation ComparisON
por: Kalkatawi, Manal, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_7ov5e1tg2mhpam6e2ipismo4im