Evidence map›Paper›PMID 29940847›Full record

ArticleBMC bioinformatics2018

ToTem: a tool for variant calling pipeline optimization.

Nikola Tom, Ondrej Tom, Jitka Malcikova, Sarka Pavlova, Blanka Kubesova, Tobias Rausch, Miroslav Kolarik, Vladimir Benes, Vojtech Bystry, Sarka Pospisilova

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In one paragraph

Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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.

Nikola TomCenter of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.ORCID 0000-0001-7440-0515
Ondrej TomDepartment of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic.
Jitka MalcikovaCenter of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
Sarka PavlovaCenter of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
Blanka KubesovaDepartment of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic.
Tobias RauschGenomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.
Miroslav KolarikDepartment of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic.
Vladimir BenesGenomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.
Vojtech BystryCenter of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic. vojtech.bystry@ceitec.muni.cz.
Sarka PospisilovaCenter of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic. pospisilova.sarka@fnbrno.cz.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundHigh-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall.

resultsHere we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data.

conclusionsToTem is a tool for automated pipeline optimization which is freely available as a web application at  https://totem.software .

Indexed as

Computational BiologyHigh-Throughput Nucleotide SequencingReproducibility of ResultsResearch DesignSoftwareBenchmarkingNext generation sequencingParameter optimizationVariant calling

Identifiers

PMID29940847
PMCPMC6020218

What OpenQuestion holds

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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.