(Q30454551)

23 September 2017

Sequencing platform and library preparation choices impact viral metagenomes (English)

1 reference

23 September 2017

Adriana Alberti

3

0 references

Gene W. Tyson

object named as

Gene Tyson

7

0 references

Corinne Cruaud

4

object named as

Corinne Cruaud

1 reference

23 September 2017

5

Steven Hallam

1 reference

23 September 2017

8

Patrick Wincker

1 reference

Konstantinos T. Konstantinidis

23 September 2017

6

object named as

Kostas Konstantinidis

1 reference

23 September 2017

Sergei A Solonenko

1

1 reference

23 September 2017

J César Ignacio-Espinoza

2

1 reference

23 September 2017

Matthew B Sullivan

9

1 reference

23 September 2017

language of work or name

English

0 references

publication date

10 May 2013

1 reference

23 September 2017

1 reference

23 September 2017

14

1 reference

23 September 2017

320

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-14-320

23 September 2017

0 references

cites work

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

VIROME: a standard operating procedure for analysis of viral metagenome sequences.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Ultrafast clustering algorithms for metagenomic sequence analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Unlocking the potential of metagenomics through replicated experimental design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Nanopores: A journey towards DNA sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Performance comparison of benchtop high-throughput sequencing platforms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Summarizing and correcting the GC content bias in high-throughput sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Individual genome assembly from complex community short-read metagenomic datasets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

A holistic approach to marine eco-systems biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

An integrated semiconductor device enabling non-optical genome sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Linear amplification for deep sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Probing individual environmental bacteria for viruses by using microfluidic digital PCR.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Field guide to next-generation DNA sequencers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Artificial duplicate reads in sequencing data of 454 Genome Sequencer FLX System

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

High-throughput DNA sequencing--concepts and limitations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

A global network of coexisting microbes from environmental and whole-genome sequence data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Recent advances in DNA sequencing methods - general principles of sample preparation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Sequencing technologies - the next generation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

New dimensions of the virus world discovered through metagenomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Large insert environmental genomic library production

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

A large genome center's improvements to the Illumina sequencing system

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Metagenomics: read length matters

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655917

Population genomics of early events in the ecological differentiation of bacteria.

20 June 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-320

Multiple displacement amplification compromises quantitative analysis of metagenomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-320

Metavir: a web server dedicated to virome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-320

Optimization of DNA extraction from low-yield and degraded samples using the BioRobot EZ1 and BioRobot M48.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-320

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-320

Systematic artifacts in metagenomes from complex microbial communities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-320

21 January 2018

Identifiers

DOI

10.1186/1471-2164-14-320

1 reference

Dimensions Publication ID

23 September 2017

0 references

1 reference

23 September 2017

PubMed publication ID

23663384

1 reference