Assembling single-cell genomes and mini-metagenomes from chimeric MDA products (Q35007840)

5 August 2017

title

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products (English)

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5 August 2017

14

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6

Alla Lapidus

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Ramunas Stepanauskas

11

Ramunas Stepanauskas

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Tanja Woyke

13

Tanja Woyke

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Anton Bankevich

Anton Bankevich

2

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Alexander V. Sirotkin

Alexander Sirotkin

9

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Alexey A. Gurevich

Alexey A Gurevich

4

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Anton Korobeynikov

Anton Korobeynikov

5

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Scott R Clingenpeel

Scott R Clingenpeel

12

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Max A. Alekseyev

Max A Alekseyev

17

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Roger S Lasken

15

Roger Lasken

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5 August 2017

18

Pavel A Pevzner

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5 August 2017

Sergey Nurk

1

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5 August 2017

Dmitry Antipov

3

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5 August 2017

Andrey D Prjibelski

7

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5 August 2017

Alexey Pyshkin

8

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Yakov Sirotkin

10

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5 August 2017

Glenn Tesler

16

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5 August 2017

publication date

1 October 2013

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Journal of Computational Biology

5 August 2017

published in

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5 August 2017

volume

20

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5 August 2017

issue

10

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5 August 2017

page(s)

714-737

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Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

5 August 2017

cites work

1 reference

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Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

8 July 2018

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Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

8 July 2018

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QUAST: quality assessment tool for genome assemblies

8 July 2018

1 reference

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An integrated pipeline for de novo assembly of microbial genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Single cell genomics: an individual look at microbes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Genomic sequencing of uncultured microorganisms from single cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Novel bacterial taxa in the human microbiome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Analyses of the microbial diversity across the human microbiome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Structure, function and diversity of the healthy human microbiome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

How to apply de Bruijn graphs to genome assembly

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Decontamination of MDA reagents for single cell whole genome amplification

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Complete genome sequence of Meiothermus ruber type strain (21)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3).

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

A catalog of reference genomes from the human microbiome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

De novo assembly of human genomes with massively parallel short read sequencing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Assembling the marine metagenome, one cell at a time

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

ABySS: a parallel assembler for short read sequence data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Single-cell genomic sequencing using Multiple Displacement Amplification

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Mechanism of chimera formation during the Multiple Displacement Amplification reaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Metagenomics: DNA sequencing of environmental samples.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

The Uncultured Microbial Majority

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

The complete genome sequence of Escherichia coli K-12

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

Telescoper: de novo assembly of highly repetitive regions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

De novo fragment assembly with short mate-paired reads: Does the read length matter?

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3791033

26 October 2018

Identifiers

DOI

10.1089/CMB.2013.0084

1 reference

journals/jcb/NurkBAGKLPPSSSCWMLTAP13

5 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

5 August 2017

1 reference