Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160).

BMC bioinformatics - 23 Nov 2025

Djaout El Hacene, Cluzel Nicolas, Marechal Vincent, Nuel Gregory, Courbariaux Marie

Abstract excerpt

BACKGROUND : Wastewater-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. RESULTS :...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Algorithms
Share to COVID-19
Share to High-Throughput Nucleotide Sequencing

Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

Share to Mutation

Share to SARS-CoV-2

Share to Software

Share to Wastewater

Source

Open in PubMed Open full text

Identifiers

PMID: 41276809
DOI: 10.1186/s12859-025-06299-7
PMCID: PMC12751500

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 8 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160).PMID 41276809Read ↗

Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samplesSemantic proximity Read ↗

VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater SamplesSemantic proximity Read ↗

Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniquesSemantic proximity Read ↗

Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, GreeceSemantic proximity Read ↗

Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, GreeceSemantic proximity Read ↗

Reconstructing SARS-CoV-2 lineages from mixed wastewater sequencing dataSemantic proximity Read ↗

Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencingSemantic proximity Read ↗

Unsupervised detection of SARS-CoV-2 mutations and lineages in Norwegian wastewater samples using long-read sequencingSemantic proximity Read ↗

Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing DataSemantic proximity Read ↗

WEPP: Phylogenetic Placement Achieves Near-Haplotype Resolution in Wastewater-Based EpidemiologySemantic proximity Read ↗

Learning novel SARS-CoV-2 lineages from wastewater sequencing dataSemantic proximity Read ↗

Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with<i>LolliPop</i>Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.