SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing (Q46248684)

27 June 2018

title

SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing (English)

1 reference

27 June 2018

1 reference

Nicholas J Hathaway

1

1 reference

27 June 2018

Christian M Parobek

series ordinal

2

1 reference

27 June 2018

Jonathan J Juliano

series ordinal

3

1 reference

27 June 2018

Jeffrey A Bailey

series ordinal

4

1 reference

27 June 2018

language of work or name

English

0 references

publication date

1 February 2018

1 reference

27 June 2018

published in

Nucleic Acids Research

1 reference

27 June 2018

volume

46

1 reference

27 June 2018

issue

4

1 reference

27 June 2018

page(s)

e21

1 reference

27 June 2018

Creative Commons Attribution 4.0 International

copyright license

start time

30 November 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

DADA2: High-resolution sample inference from Illumina amplicon data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

The vaginal microbiome during pregnancy and the postpartum period in a European population.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

MetAmp: combining amplicon data from multiple markers for OTU analysis

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Genetic architecture of artemisinin-resistant Plasmodium falciparum

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Swarm: robust and fast clustering method for amplicon-based studies

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

UPARSE: highly accurate OTU sequences from microbial amplicon reads

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Analysis of circulating tumor DNA to monitor metastatic breast cancer

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Inferring correlation networks from genomic survey data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Efficient error correction for next-generation sequencing of viral amplicons

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

A survey of error-correction methods for next-generation sequencing

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Ultra-deep sequencing for the analysis of viral populations

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

ART: a next-generation sequencing read simulator.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

An efficient simulator of 454 data using configurable statistical models

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

FLASH: fast length adjustment of short reads to improve genome assemblies

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Removing noise from pyrosequenced amplicons

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

An SNP map of the human genome generated by reduced representation shotgun sequencing

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

Fast, accurate error-correction of amplicon pyrosequences using Acacia.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5829576

15 August 2018

Identifiers

DOI

10.1093/NAR/GKX1201

1 reference

27 June 2018

PMC publication ID

5829576

1 reference

27 June 2018

PubMed publication ID

29202193

1 reference

27 June 2018