4.6 Article

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

John Beaulaurier et al.

GENOME RESEARCH (2020)

Article Multidisciplinary Sciences

Clades of huge phages from across Earth's ecosystems

Basem Al-Shayeb et al.

NATURE (2020)

Article Biotechnology & Applied Microbiology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

Eli L. Moss et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

yacrd and fpa: upstream tools for long-read genome assembly

Pierre Marijon et al.

BIOINFORMATICS (2020)

Review Biotechnology & Applied Microbiology

Opportunities and challenges in long-read sequencing data analysis

Shanika L. Amarasinghe et al.

GENOME BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Ann C. Gregory et al.

Article Biotechnology & Applied Microbiology

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov et al.

NATURE BIOTECHNOLOGY (2019)

Article Microbiology

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

Andrey N. Shkoporov et al.

CELL HOST & MICROBE (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemical Research Methods

NanoPack: visualizing and processing long-read sequencing data

Wouter De Coster et al.

BIOINFORMATICS (2018)

Article Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

Joanne B. Emerson et al.

NATURE MICROBIOLOGY (2018)

Article Biochemistry & Molecular Biology

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk et al.

GENOME RESEARCH (2017)

Article Biochemistry & Molecular Biology

Fast and accurate de novo genome assembly from long uncorrected reads

Robert Vaser et al.

GENOME RESEARCH (2017)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Review Microbiology

Menage a trois in the human gut: interactions between host, bacteria and phages

Mohammadali Khan Mirzaei et al.

NATURE REVIEWS MICROBIOLOGY (2017)

Article Multidisciplinary Sciences

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

Francisco Martinez-Hernandez et al.

NATURE COMMUNICATIONS (2017)

Article Microbiology

Jumbo Bacteriophages:An Overview

Yihui Yuan et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Microbiology

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

Melissa B. Duhaime et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Biochemical Research Methods

BCFtools/csq: haplotype-aware variant consequences

Petr Danecek et al.

BIOINFORMATICS (2017)

Article Biotechnology & Applied Microbiology

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

William C. Nelson et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biochemical Research Methods

HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads

Dmitry Antipov et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

Heng Li

BIOINFORMATICS (2016)

Article Multidisciplinary Sciences

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Simon Roux et al.

NATURE (2016)

Article Multidisciplinary Sciences

Redefining the invertebrate RNA virosphere

Mang Shi et al.

NATURE (2016)

Review Microbiology

Rising to the challenge: accelerated pace of discovery transforms marine virology

Jennifer R. Brum et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Multidisciplinary Sciences

Patterns and ecological drivers of ocean viral communities

Jennifer R. Brum et al.

SCIENCE (2015)

Article Multidisciplinary Sciences

VirSorter: mining viral signal from microbial genomic data

Simon Roux et al.

PEERJ (2015)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Environmental Sciences

A simple and efficient method for concentration of ocean viruses by chemical flocculation

Seth G. John et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2011)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Genomic analysis of uncultured marine viral communities

M Breitbart et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)