标题
New approaches for metagenome assembly with short reads
作者
关键词
-
出版物
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages -
出版商
Oxford University Press (OUP)
发表日期
2019-02-05
DOI
10.1093/bib/bbz020
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
- (2018) Robert D. Stewart et al. Nature Communications
- De novo assembly of viral quasispecies using overlap graphs
- (2017) Jasmijn A. Baaijens et al. GENOME RESEARCH
- metaSPAdes: a new versatile metagenomic assembler
- (2017) Sergey Nurk et al. GENOME RESEARCH
- Direct determination of diploid genome sequences
- (2017) Neil I. Weisenfeld et al. GENOME RESEARCH
- Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation
- (2017) Sergey Koren et al. GENOME RESEARCH
- A world of opportunities with nanopore sequencing
- (2017) Richard M Leggett et al. JOURNAL OF EXPERIMENTAL BOTANY
- Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
- (2017) Alexander Sczyrba et al. NATURE METHODS
- EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
- (2017) Alex L Mitchell et al. NUCLEIC ACIDS RESEARCH
- Metagenomics of microbial and viral life in terrestrial geothermal environments
- (2017) Andrea Strazzulli et al. REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY
- Metagenomics of microbial and viral life in terrestrial geothermal environments
- (2017) Andrea Strazzulli et al. REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY
- Snowball: strain aware gene assembly of metagenomes
- (2016) I. Gregor et al. BIOINFORMATICS
- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
- (2016) Heng Li BIOINFORMATICS
- BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly
- (2016) Ka-Kit Lam et al. BMC BIOINFORMATICS
- MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression
- (2016) Minji Kim et al. BMC BIOINFORMATICS
- Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
- (2016) Nicholas H. Putnam et al. GENOME RESEARCH
- MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
- (2016) Dinghua Li et al. METHODS
- Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
- (2016) J. A. Frank et al. Scientific Reports
- Characterization of a Zika Virus Isolate from Colombia
- (2016) Anismrita Lahon et al. PLoS Neglected Tropical Diseases
- Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
- (2016) Ankit Gupta et al. Frontiers in Microbiology
- Back to the Future of Soil Metagenomics
- (2016) Joseph Nesme et al. Frontiers in Microbiology
- RAMPART: a workflow management system for de novo genome assembly
- (2015) Daniel Mapleson et al. BIOINFORMATICS
- IVA: accuratede novoassembly of RNA virus genomes
- (2015) Martin Hunt et al. BIOINFORMATICS
- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- MetaQUAST: evaluation of metagenome assemblies
- (2015) Alla Mikheenko et al. BIOINFORMATICS
- BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
- (2015) Felipe A. Simão et al. BIOINFORMATICS
- InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
- (2015) Binbin Lai et al. BMC BIOINFORMATICS
- Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease
- (2015) Jason M. Norman et al. CELL
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013
- (2015) Simon J. Watson et al. JOURNAL OF VIROLOGY
- A new antibiotic kills pathogens without detectable resistance
- (2015) Losee L. Ling et al. NATURE
- An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data
- (2015) Xutao Deng et al. NUCLEIC ACIDS RESEARCH
- Structure and function of the global ocean microbiome
- (2015) S. Sunagawa et al. SCIENCE
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
- (2015) Dongwan D. Kang et al. PeerJ
- Xander: employing a novel method for efficient gene-targeted metagenomic assembly
- (2015) Qiong Wang et al. Microbiome
- Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
- (2015) Ebrahim Afshinnekoo et al. Cell Systems
- Omega: an Overlap-graph de novo Assembler for Metagenomics
- (2014) Bahlul Haider et al. BIOINFORMATICS
- Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
- (2014) Jorge F Vázquez-Castellanos et al. BMC GENOMICS
- MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
- (2014) Afiahayati et al. DNA RESEARCH
- REVIEW: On the species abundance distribution in applied ecology and biodiversity management
- (2014) Thomas J. Matthews et al. JOURNAL OF APPLIED ECOLOGY
- Binning metagenomic contigs by coverage and composition
- (2014) Johannes Alneberg et al. NATURE METHODS
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- (2014) Bruce J. Walker et al. PLoS One
- Tackling soil diversity with the assembly of large, complex metagenomes
- (2014) Adina Chuang Howe et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metagenomic shotgun sequencing of a Bunyavirus in wild-caught Aedes aegypti from Thailand informs the evolutionary and genomic history of the Phleboviruses
- (2014) James Angus Chandler et al. VIROLOGY
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- Space-efficient and exact de Bruijn graph representation based on a Bloom filter
- (2013) Rayan Chikhi et al. Algorithms for Molecular Biology
- ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
- (2013) Scott C. Clark et al. BIOINFORMATICS
- Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants
- (2013) Thomas R Turner et al. ISME Journal
- Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data
- (2013) Aarti Desai et al. PLoS One
- Metagenomic study of the viruses of African straw-coloured fruit bats: Detection of a chiropteran poxvirus and isolation of a novel adenovirus
- (2013) Kate S. Baker et al. VIROLOGY
- PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data
- (2013) J. Graham Ruby et al. G3-Genes Genomes Genetics
- The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
- (2013) Sara C Di Rienzi et al. eLife
- MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
- (2013) Todd J Treangen et al. GENOME BIOLOGY
- An extended genovo metagenomic assembler by incorporating paired-end information
- (2013) Afiahayati et al. PeerJ
- A de novo metagenomic assembly program for shotgun DNA reads
- (2012) Binbin Lai et al. BIOINFORMATICS
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- De novo assembly of highly diverse viral populations
- (2012) Xiao Yang et al. BMC GENOMICS
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
- (2012) Toshiaki Namiki et al. NUCLEIC ACIDS RESEARCH
- Ray Meta: scalable de novo metagenome assembly and profiling
- (2012) Sébastien Boisvert et al. GENOME BIOLOGY
- Genovo: De Novo Assembly for Metagenomes
- (2011) Jonathan Laserson et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Meraculous: De Novo Genome Assembly with Short Paired-End Reads
- (2011) Jarrod A. Chapman et al. PLoS One
- Unsupervised statistical clustering of environmental shotgun sequences
- (2009) Andrey Kislyuk et al. BMC BIOINFORMATICS
- ABySS: A parallel assembler for short read sequence data
- (2009) J. T. Simpson et al. GENOME RESEARCH
- De novo assembly of human genomes with massively parallel short read sequencing
- (2009) R. Li et al. GENOME RESEARCH
- Maximum Likelihood Genome Assembly
- (2009) Paul Medvedev et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started