Cargando…

Capturing variation in metagenomic assembly graphs with MetaCortex

MOTIVATION: The assembly of contiguous sequence from metagenomic samples presents a particular challenge, due to the presence of multiple species, often closely related, at varying levels of abundance. Capturing diversity within species, for example, viral haplotypes, or bacterial strain-level diver...

Descripción completa

Detalles Bibliográficos
Autores principales:	Martin, Samuel, Ayling, Martin, Patrono, Livia, Caccamo, Mario, Murcia, Pablo, Leggett, Richard M
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Original Paper
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9889960/ https://www.ncbi.nlm.nih.gov/pubmed/36722204 http://dx.doi.org/10.1093/bioinformatics/btad020

Ejemplares similares

New approaches for metagenome assembly with short reads
por: Ayling, Martin, et al.
Publicado: (2019)

Metagenomic binning with assembly graph embeddings
por: Lamurias, Andre, et al.
Publicado: (2022)

STRONG: metagenomics strain resolution on assembly graphs
por: Quince, Christopher, et al.
Publicado: (2021)

De novo assembly and genotyping of variants using colored de Bruijn graphs
por: Iqbal, Zamin, et al.
Publicado: (2012)

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
por: Ye, Yuzhen, et al.
Publicado: (2016)

Improving metagenomic binning results with overlapped bins using assembly graphs
por: Mallawaarachchi, Vijini G., et al.
Publicado: (2021)

ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs
por: Dvorkina, Tatiana, et al.
Publicado: (2021)

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
por: Zhang, Zhenmiao, et al.
Publicado: (2021)

StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs
por: Da Silva, Kévin, et al.
Publicado: (2021)

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
por: Brown, C. Titus, et al.
Publicado: (2020)

Metazen – metadata capture for metagenomes
por: Bischof, Jared, et al.
Publicado: (2014)

Phylogenetically distinct equine influenza viruses show different tropism for the swine respiratory tract
por: Patrono, Livia V., et al.
Publicado: (2015)

Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
por: García-López, Rodrigo, et al.
Publicado: (2015)

MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs
por: Li, Dinghua, et al.
Publicado: (2017)

Metagenomic study of the viruses of African straw-coloured fruit bats: Detection of a chiropteran poxvirus and isolation of a novel adenovirus
por: Baker, Kate S., et al.
Publicado: (2013)

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs
por: Leggett, Richard M., et al.
Publicado: (2013)

Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs
por: Benoit, Gaëtan, et al.
Publicado: (2023)

Graph colouring and variations
por: de Werra, D, et al.
Publicado: (1989)

Gramtools enables multiscale variation analysis with genome graphs
por: Letcher, Brice, et al.
Publicado: (2021)

Characterization of metagenome-assembled genomes from the International Space Station
por: Singh, Nitin K., et al.
Publicado: (2023)

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes
por: Guitor, Allison K., et al.
Publicado: (2019)

OGRE: Overlap Graph-based metagenomic Read clustEring
por: Balvert, Marleen, et al.
Publicado: (2020)

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data
por: Daly, Gordon M., et al.
Publicado: (2015)

Non‐invasive genomics of respiratory pathogens infecting wild great apes using hybridisation capture
por: Patrono, Livia V., et al.
Publicado: (2022)

High-throughput microbial population genomics using the Cortex variation assembler
por: Iqbal, Zamin, et al.
Publicado: (2013)

metaSPAdes: a new versatile metagenomic assembler
por: Nurk, Sergey, et al.
Publicado: (2017)

Exome capture from saliva produces high quality genomic and metagenomic data
por: Kidd, Jeffrey M, et al.
Publicado: (2014)

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
por: Martin, Samuel, et al.
Publicado: (2022)

Assembly of Bacterial Genomes from the Metagenomes of Three Lichen Species
por: Wicaksono, Wisnu Adi, et al.
Publicado: (2020)

Graph pangenome captures missing heritability and empowers tomato breeding
por: Zhou, Yao, et al.
Publicado: (2022)

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans
por: Duncan, Anthony, et al.
Publicado: (2022)

MetaCarvel: linking assembly graph motifs to biological variants
por: Ghurye, Jay, et al.
Publicado: (2019)

Metagenomic Assembly and Prokaryotic Metagenome-Assembled Genome Sequences from the Northern Gulf of Mexico “Dead Zone”
por: Thrash, J. Cameron, et al.
Publicado: (2018)

Metagenome Assembly and Metagenome-Assembled Genome Sequences from the Rhizosphere of Maize Plants in Mafikeng, South Africa
por: Babalola, Olubukola O., et al.
Publicado: (2021)

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
por: Metsky, Hayden C., et al.
Publicado: (2019)

Probe design for simultaneous, targeted capture of diverse metagenomic targets
por: Dickson, Zachery W., et al.
Publicado: (2021)

Probe design for simultaneous, targeted capture of diverse metagenomic targets
por: Dickson, Zachery W., et al.
Publicado: (2022)

Meta-IDBA: a de Novo assembler for metagenomic data
por: Peng, Yu, et al.
Publicado: (2011)

Ray Meta: scalable de novo metagenome assembly and profiling
por: Boisvert, Sébastien, et al.
Publicado: (2012)

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights
por: Warnke-Sommer, Julia, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_jqvp90p5i5eamhl347mi0ojgis