Evidence map›Paper›PMID 25478564›Full record

ArticleInternational journal of genomics2014

Facile, high quality sequencing of bacterial genomes from small amounts of DNA.

Momchilo Vuyisich, Ayesha Arefin, Karen Davenport, Shihai Feng, Cheryl Gleasner, Kim McMurry, Beverly Parson-Quintana, Jennifer Price, Matthew Scholz, Patrick Chain

Abstract read
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Article in International journal of genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Momchilo VuyisichLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Ayesha ArefinLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Karen DavenportLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Shihai FengLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Cheryl GleasnerLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Kim McMurryLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Beverly Parson-QuintanaLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Jennifer PriceParkview Medical Center School for Medical Laboratory Science, 400 West 16th Street, Pueblo, CO 81003, USA.
Matthew ScholzLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Patrick ChainLos Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used.

Identifiers

PMID25478564
PMCPMC4247979

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.