ArticleBMC bioinformatics2025
Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160).
Article in BMC bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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.
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.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWastewater-based epidemiology has been investigated as a very effective way of monitoring SARS-CoV-2 variants. This can be achieved through accurate lineage deconvolution of wastewater sequencing data. Variants Ratios from Pooled Sequencing (VaRaPS) is a Python package designed for this purpose, utilizing pooled sequencing data and lineage mutation profiles to estimate their proportions.
resultsVaRaPS re-implements core algorithms from the literature, achieving significant improvements in computational speed and efficiency. Comparative analyzes with simulated and synthetic data sets demonstrate its superior performance in lineage prevalence estimation, underscored by its user-oriented design for broader accessibility.
conclusionsBy improving speed and accuracy in SARS-CoV-2 variant analysis, VaRaPS offers valuable insights into viral evolution, supporting ongoing surveillance efforts in the post-pandemic landscape.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.