Strainberry: automated strain separation in low-complexity metagenomes using long reads
出版年份 2021 全文链接
标题
Strainberry: automated strain separation in low-complexity metagenomes using long reads
作者
关键词
-
出版物
Nature Communications
Volume 12, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2021-07-23
DOI
10.1038/s41467-021-24515-9
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。- Complete, closed bacterial genomes from microbiomes using nanopore sequencing
- (2020) Eli L. Moss et al. NATURE BIOTECHNOLOGY
- SciPy 1.0: fundamental algorithms for scientific computing in Python
- (2020) Pauli Virtanen et al. NATURE METHODS
- Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
- (2020) Kishwar Shafin et al. NATURE BIOTECHNOLOGY
- Diversity within species: interpreting strains in microbiomes
- (2020) Thea Van Rossum et al. NATURE REVIEWS MICROBIOLOGY
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study
- (2020) Adriel Latorre-Pérez et al. Scientific Reports
- Array programming with NumPy
- (2020) Charles R. Harris et al. NATURE
- metaFlye: scalable long-read metagenome assembly using repeat graphs
- (2020) Mikhail Kolmogorov et al. NATURE METHODS
- Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data
- (2020) Christine Anyansi et al. Frontiers in Microbiology
- Chromosome-scale, haplotype-resolved assembly of human genomes
- (2020) Shilpa Garg et al. NATURE BIOTECHNOLOGY
- Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
- (2020) David Porubsky et al. NATURE BIOTECHNOLOGY
- Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
- (2019) Vincent Somerville et al. BMC MICROBIOLOGY
- Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
- (2019) Denis Bertrand et al. NATURE BIOTECHNOLOGY
- MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
- (2019) Dongwan D. Kang et al. PeerJ
- Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
- (2019) Robert D. Stewart et al. NATURE BIOTECHNOLOGY
- Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing
- (2019) Peter Edge et al. Nature Communications
- Fast and accurate long-read assembly with wtdbg2
- (2019) Jue Ruan et al. NATURE METHODS
- Minimap2: pairwise alignment for nucleotide sequences
- (2018) Heng Li BIOINFORMATICS
- MUMmer4: A fast and versatile genome alignment system
- (2018) Guillaume Marçais et al. PLoS Computational Biology
- On the Road to Strain-Resolved Comparative Metagenomics
- (2018) Nicola Segata mSystems
- De novo assembly of viral quasispecies using overlap graphs
- (2017) Jasmijn A. Baaijens et al. GENOME RESEARCH
- Microbial strain-level population structure and genetic diversity from metagenomes
- (2017) Duy Tin Truong et al. GENOME RESEARCH
- Fast and accurate de novo genome assembly from long uncorrected reads
- (2017) Robert Vaser 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
- Strain profiling and epidemiology of bacterial species from metagenomic sequencing
- (2017) Davide Albanese et al. Nature Communications
- Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
- (2017) Donovan H. Parks et al. Nature Microbiology
- Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis
- (2017) Adrian Tett et al. npj Biofilms and Microbiomes
- HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
- (2016) Peter Edge et al. GENOME RESEARCH
- Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.
- (2015) Ryan R. Wick et al. BIOINFORMATICS
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- ConStrains identifies microbial strains in metagenomic datasets
- (2015) Chengwei Luo et al. NATURE BIOTECHNOLOGY
- Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
- (2015) Brian Cleary et al. NATURE BIOTECHNOLOGY
- QUAST: quality assessment tool for genome assemblies
- (2013) Alexey Gurevich et al. BIOINFORMATICS
- GAGE: A critical evaluation of genome assemblies and assembly algorithms
- (2011) S. L. Salzberg et al. GENOME RESEARCH
- Epidemic Profile of Shiga-Toxin–ProducingEscherichia coliO104:H4 Outbreak in Germany
- (2011) Christina Frank et al. NEW ENGLAND JOURNAL OF MEDICINE
- Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells
- (2010) G. Cuevas-Ramos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Biopython: freely available Python tools for computational molecular biology and bioinformatics
- (2009) P. J. A. Cock et al. BIOINFORMATICS
- Circos: An information aesthetic for comparative genomics
- (2009) M. Krzywinski et al. GENOME RESEARCH
- A comparison of homologous recombination rates in bacteria and archaea
- (2008) Michiel Vos et al. ISME Journal
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started