Evidence map›Paper›PMID 35075458›Full record

ArticlebioRxiv : the preprint server for biology2022

RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis.

Alexander G Lucaci, Jordan D Zehr, Stephen D Shank, Dave Bouvier, Han Mei, Anton Nekrutenko, Darren P Martin, Sergei L Kosakovsky Pond

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2022. 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

5 · Who and what money

Authors and funding

8 authors.

Alexander G LucaciInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA.
Jordan D ZehrInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA.
Stephen D ShankInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA.
Dave BouvierDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Han MeiDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Anton NekrutenkoDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Darren P MartinInstitute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa.
Sergei L Kosakovsky PondInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA.

Funding

Turning big data analysis infrastructure for HIV researchR01AI134384 · NIAID · PENNSYLVANIA STATE UNIVERSITY, THE · PI NEKRUTENKO, ANTON, POND, SERGEI L KOSAKOVSKY · 2017 to 2021
$4.2M
NIAID NIH HHS R01 AI134384Wellcome Trust
6 · The paper itself

Abstract

An important component of efforts to manage the ongoing COVID19 pandemic is the R apid A ssessment of how natural selection contributes to the emergence and proliferation of potentially dangerous S ARS-CoV-2 lineages and CL ades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations. AVAILABILITY: RASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl . Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl . CONTACT: Dr. Sergei L Kosakovsky Pond ( spond@temple.edu ). SUPPLEMENTARY INFORMATION: N/A.

Identifiers

PMID35075458
PMCPMC8786235

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

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.