Evidence map›Paper›PMID 35771206›Full record

ArticleMicrobial genomics2022

Catwalk: identifying closely related sequences in large microbial sequence databases.

Denis Volk, Fan Yang-Turner, Xavier Didelot, Derrick W Crook, David Wyllie

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 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, top 91% of its field
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, 0 citations in OpenAlex.

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

5 authors at 4 institutions in 1 country.

Denis VolkNuffield Department of Medicine, University of Oxford, Oxford, UK.
Fan Yang-TurnerNuffield Department of Medicine, University of Oxford, Oxford, UK.
Xavier DidelotSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
Derrick W CrookNuffield Department of Medicine, University of Oxford, Oxford, UK.
David WyllieUK Health Security Agency, Forvie Site, Addenbrookes' Campus, Robinson Way, Cambridge CB2 0SR, UK.
University of Oxford · GBScience and Technology Facilities Council · GBUK Health Security Agency · GBUniversity of Warwick · GB

Funding

Wellcome TrustWellcome Trust 215800/Z/19/Z
6 · The paper itself

Abstract

There is a need to identify microbial sequences that may form part of transmission chains, or that may represent importations across national boundaries, amidst large numbers of SARS-CoV-2 and other bacterial or viral sequences. Reference-based compression is a sequence analysis technique that allows both a compact storage of sequence data and comparisons between sequences. Published implementations of the approach are being challenged by the large sample collections now being generated. Our aim was to develop a fast software detecting highly similar sequences in large collections of microbial genomes, including millions of SARS-CoV-2 genomes. To do so, we developed Catwalk, a tool that bypasses bottlenecks in the generation, comparison and in-memory storage of microbial genomes generated by reference mapping. It is a compiled solution, coded in Nim to increase performance. It can be accessed via command line, rest api or web server interfaces. We tested Catwalk using both SARS-CoV-2 and

Indexed as

COVID-19Mycobacterium tuberculosisDatabases, Nucleic AcidHumansProspective StudiesSARS-CoV-2Softwarebacterial genomicsmicrobial relatednessoutbreak detection

Identifiers

PMID35771206
PMCPMC9455716
OpenAlexW4283742305

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.