Cargando…

IVA: accurate de novo assembly of RNA virus genomes

Motivation: An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challen...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hunt, Martin, Gall, Astrid, Ong, Swee Hoe, Brener, Jacqui, Ferns, Bridget, Goulder, Philip, Nastouli, Eleni, Keane, Jacqueline A., Kellam, Paul, Otto, Thomas D.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2015
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495290/ https://www.ncbi.nlm.nih.gov/pubmed/25725497 http://dx.doi.org/10.1093/bioinformatics/btv120

Ejemplares similares

Disease progression despite protective HLA expression in an HIV-infected transmission pair
por: Brener, Jacqui, et al.
Publicado: (2015)

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes
por: Bassano, Irene, et al.
Publicado: (2017)

ABACAS: algorithm-based automatic contiguation of assembled sequences
por: Assefa, Samuel, et al.
Publicado: (2009)

Bandage: interactive visualization of de novo genome assemblies
por: Wick, Ryan R., et al.
Publicado: (2015)

Emergence of a novel subclade of influenza A(H3N2) virus in London, December 2016 to January 2017
por: Harvala, Heli, et al.
Publicado: (2017)

RAMPART: a workflow management system for de novo genome assembly
por: Mapleson, Daniel, et al.
Publicado: (2015)

Rapid HIV disease progression following superinfection in an HLA-B*27:05/B*57:01-positive transmission recipient
por: Brener, Jacqui, et al.
Publicado: (2018)

PGPointNovo: an efficient neural network-based tool for parallel de novo peptide sequencing
por: Xu, Xiaofang, et al.
Publicado: (2023)

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data
por: Page, Andrew J., et al.
Publicado: (2016)

Roary: rapid large-scale prokaryote pan genome analysis
por: Page, Andrew J., et al.
Publicado: (2015)

Diagnosing mucopolysaccharidosis IVA
por: Wood, Timothy C., et al.
Publicado: (2013)

Fast and accurate prediction of protein side-chain conformations
por: Liang, Shide, et al.
Publicado: (2011)

SonicParanoid: fast, accurate and easy orthology inference
por: Cosentino, Salvatore, et al.
Publicado: (2019)

compleasm: a faster and more accurate reimplementation of BUSCO
por: Huang, Neng, et al.
Publicado: (2023)

SMuRF: portable and accurate ensemble prediction of somatic mutations
por: Huang, Weitai, et al.
Publicado: (2019)

MAGScoT: a fast, lightweight and accurate bin-refinement tool
por: Rühlemann, Malte Christoph, et al.
Publicado: (2022)

Unfazed: parent-of-origin detection for large and small de novo variants
por: Belyeu, Jonathan R, et al.
Publicado: (2021)

nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning
por: Alharbi, Bader A., et al.
Publicado: (2014)

Precrec: fast and accurate precision–recall and ROC curve calculations in R
por: Saito, Takaya, et al.
Publicado: (2017)

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing
por: Mohiyuddin, Marghoob, et al.
Publicado: (2015)

FATHMM-XF: accurate prediction of pathogenic point mutations via extended features
por: Rogers, Mark F, et al.
Publicado: (2018)

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
por: Zielezinski, Andrzej, et al.
Publicado: (2021)

COT: an efficient and accurate method for detecting marker genes among many subtypes
por: Lu, Yingzhou, et al.
Publicado: (2022)

DOCEST—fast and accurate estimator of human NGS sequencing depth and error rate
por: Kaplinski, Lauris, et al.
Publicado: (2023)

Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data
por: Dunn, Tamsen, et al.
Publicado: (2019)

YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells
por: Lu, Alex X, et al.
Publicado: (2019)

Steer’n’Detect: fast 2D template detection with accurate orientation estimation
por: Uhlmann, Virginie, et al.
Publicado: (2022)

ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data
por: Chen, Shengquan, et al.
Publicado: (2022)

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
por: Walters, William A., et al.
Publicado: (2011)

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments
por: van Heeringen, Simon J., et al.
Publicado: (2011)

CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes
por: Shen, Yin, et al.
Publicado: (2021)

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
por: Naeem, Raeece, et al.
Publicado: (2013)

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
por: Coll, Francesc, et al.
Publicado: (2012)

EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing
por: Berndsen, Zachary, et al.
Publicado: (2017)

DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences
por: Jeske, Tim, et al.
Publicado: (2019)

Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions
por: Ribeiro, Judemir, et al.
Publicado: (2019)

MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data
por: Fosso, B, et al.
Publicado: (2017)

Reference‐free discovery of nuclear SNPs permits accurate, sensitive identification of Carya (hickory) species and hybrids
por: Literman, Robert A., et al.
Publicado: (2022)

DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes
por: Liu, Jun, et al.
Publicado: (2023)

Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP
por: Melo, Arthur T O, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_n192o2rf1fa1lbf5asqic3k0ef