Cargando…

MOST: a modified MLST typing tool based on short read sequencing

Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional...

Descripción completa

Detalles Bibliográficos
Autores principales:	Tewolde, Rediat, Dallman, Timothy, Schaefer, Ulf, Sheppard, Carmen L., Ashton, Philip, Pichon, Bruno, Ellington, Matthew, Swift, Craig, Green, Jonathan, Underwood, Anthony
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2016
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991843/ https://www.ncbi.nlm.nih.gov/pubmed/27602279 http://dx.doi.org/10.7717/peerj.2308

Ejemplares similares

Identification of Salmonella for public health surveillance using whole genome sequencing
por: Ashton, Philip M., et al.
Publicado: (2016)

Clinical streptococcal isolates, distinct from Streptococcus pneumoniae, but containing the β-glucosyltransferase tts gene and expressing serotype 37 capsular polysaccharide
por: Sheppard, Carmen L., et al.
Publicado: (2017)

Deconvolute individual genomes from metagenome sequences through short read clustering
por: Li, Kexue, et al.
Publicado: (2020)

Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms
por: Priest, Taylor, et al.
Publicado: (2021)

An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data
por: Bowles, Harry, et al.
Publicado: (2023)

Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline
por: Kapatai, Georgia, et al.
Publicado: (2016)

Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing
por: Ashton, Philip M., et al.
Publicado: (2015)

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
por: Zablocki, Olivier, et al.
Publicado: (2021)

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species
por: Harvey, Michael G., et al.
Publicado: (2015)

Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data
por: Cline, Eliot, et al.
Publicado: (2020)

URMAP, an ultra-fast read mapper
por: Edgar, Robert
Publicado: (2020)

Getting the most out of RNA-seq data analysis
por: Khang, Tsung Fei, et al.
Publicado: (2015)

Atropos: specific, sensitive, and speedy trimming of sequencing reads
por: Didion, John P., et al.
Publicado: (2017)

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
por: Liu, Daniel
Publicado: (2019)

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)
por: Kobayashi, Genki
Publicado: (2023)

FLAME: long-read bioinformatics tool for comprehensive spliceome characterization
por: Holmqvist, Isak, et al.
Publicado: (2021)

Massively parallel read mapping on GPUs with the q-group index and PEANUT
por: Köster, Johannes, et al.
Publicado: (2014)

The PARA-suite: PAR-CLIP specific sequence read simulation and processing
por: Kloetgen, Andreas, et al.
Publicado: (2016)

HAHap: a read-based haplotyping method using hierarchical assembly
por: Lin, Yu-Yu, et al.
Publicado: (2018)

SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading
por: Nováček, Vít, et al.
Publicado: (2014)

Improving transcriptome assembly through error correction of high-throughput sequence reads
por: MacManes, Matthew D., et al.
Publicado: (2013)

Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads
por: Ye, Chengxi, et al.
Publicado: (2016)

IterCluster: a barcode clustering algorithm for long fragment read analysis
por: Weng, Jiancong, et al.
Publicado: (2020)

kakapo: easy extraction and annotation of genes from raw RNA-seq reads
por: Ramanauskas, Karolis, et al.
Publicado: (2023)

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads
por: Roosaare, Märt, et al.
Publicado: (2018)

corseq: fast and efficient identification of favoured codons from next generation sequencing reads
por: Camiolo, Salvatore, et al.
Publicado: (2018)

Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism
por: Burri, Dominik, et al.
Publicado: (2021)

GROM-RD: resolving genomic biases to improve read depth detection of copy number variants
por: Smith, Sean D., et al.
Publicado: (2015)

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space
por: Wilton, Richard, et al.
Publicado: (2015)

Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus
por: Page, Andrew J., et al.
Publicado: (2018)

CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
por: Morlion, Annelien, et al.
Publicado: (2022)

Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data
por: DeMario, Samuel, et al.
Publicado: (2023)

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
por: Warwick-Dugdale, Joanna, et al.
Publicado: (2019)

PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2
por: Valencia-Valencia, David E., et al.
Publicado: (2022)

RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity
por: Gerhardt, Kenji, et al.
Publicado: (2022)

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters
por: Baltoumas, Fotis A., et al.
Publicado: (2023)

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
por: Roosaare, Märt, et al.
Publicado: (2017)

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
por: Andermann, Tobias, et al.
Publicado: (2018)

Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development
por: Playfoot, Christopher J., et al.
Publicado: (2022)

An improved analysis methodology for translational profiling by microarray
por: Sbarrato, Thomas, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_iujla7ddssnka0tosgcf71h1bl