Data · dataset · 2026
Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing
Listed in DataSuds
This repository contains all the files needed to reproduce the results of the article "ViroSeek: a viral detection pipeline for second-generation sequencing", including the files needed to run the ViroSeek pipeline.
Description
ViroSeek is a simplified bioinformatics pipeline for the taxonomic analysis of second-generation sequencing data. It contains: Main pipeline scripts (bash or nextflow) for automated execution of the steps Installation instructions and README file describing the software prerequisites (FastQC, TrimGalore, BBTools, SPAdes, Samtools, TaxonKit), as well as the yml file for setting up the conda environment.
Bash script for generating simulated data with CASIMIM, used as a positive sample in the article. R script used for downstream pipeline analysis
Links
Where it is published
- Dataverse dataset page dataverse.ird.fr/dataset.xhtml?persistentId=doi%3A10.23708%2FLTXIKA ↗
landing page · from dataverse ird fr
- DOI doi.org/10.23708/ltxika ↗
DOI / persistent id · from dataverse ird fr
Catalogue records · 1
- Dataverse API dataverse.ird.fr/api/datasets/:persistentId/?persistentId=doi%3A10.23708%2FLTXI… ↗
metadata API · from dataverse ird fr
Topics
- Stated by source
- Medicine, Health and Life Sciences
- From keywords
- Economics & Finance · Life Sciences · Medicine & Health
- Inferred from text
- Sequencing 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataSuds | doi:10.23708/LTXIKA | 4 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | /subjects |
| concepts[field].local:field:economics-finance | mapping · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | /subjects |
| concepts[modality].local:modality:sequencing | enrichment · dataverse ird fr | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | |
| description | source · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | /description |
| publication_date | source · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | |
| title | source · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | /name |
| updated_date | source · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 | |
| version_label | source · dataverse ird fr | connector:dataverse_ird_fr@1.0.0 |