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DATASET

Shotgun WGS dataset from 9 SARS-CoV-2 representative sequences

Collection: ETOHA-OPEN : ETOHA-OPEN - Emerging Health Threats and the One Health Approach 

Description

This dataset comprises > 100 shotgun paired-end whole genome sequencing (WGS) data generated from nine representative SARS-CoV-2 sequences (IDs: LR991699,MW617687,MW763128,MW972888,OD913776,OM873778,OM898676,OU015160,OV754178) obtained from the COVID-19 data portal (https://www.covid19dataportal.org). The WGS datasets were created using InSilicoSeq (v. 2.0.1, https://github.com/HadrienG/InSilicoSeq). For each representative sequence, we generated datasets with three different error models (HiSeq, NovaSeq, MiSeq) and read lengths (125, 150, 300 bps respectively) using the --model parameter (HiSeq, NovaSeq, MiSeq, see: https://insilicoseq.readthedocs.io/en/latest/iss/model.html). The datasets cover a range of sequencing depths, including 5x-10x, 11x-100x, 101x-1000x, and greater than 1000x. Each FASTQ file name contains information on the representative sequence ID, the InSilicoSeq error model used, and the required coverage (i.e., ID.model.coverage.fastq.gz). Sample information are also reported in the provided metadata csv file.

Contact

Email
gabriele.leoni (at) ec.europa.eu

Contributors

  • Gabriele Leoni
  • Mauro Petrillo
  • Victoria RUIZ SERRA

How to cite

Leoni, Gabriele; Petrillo, Mauro; RUIZ SERRA, Victoria (2024): Shotgun WGS dataset from 9 SARS-CoV-2 representative sequences. European Commission, Joint Research Centre (JRC) [Dataset] doi: 10.2905/f4cb0c69-5d43-4765-9ec8-e79cb28c21bc PID: http://data.europa.eu/89h/f4cb0c69-5d43-4765-9ec8-e79cb28c21bc

Keywords

Bioinformatics IN-Silico PATHOSEQ-QC Representative Sequences SARS-Cov2 WGS

Data access

Shotgun WGS dataset metadata
Use conditions
European Commission reuse notice 
Access conditions
No limitations 
Download 

  • This csv file reports information related to each shotgun in-silico generated sample, comprising coverage median, lineage data, accession ID of the original sequence and error model used.

Shotgun WGS dataset from 9 SARS-CoV-2 representative sequences
Use conditions
European Commission reuse notice 
Access conditions
No limitations 
Download 

Additional information

Published by
European Commission, Joint Research Centre
Created date
2024-10-28
Modified date
2024-11-19
Issued date
2024-10-27
Data theme(s)
Health, Science and technology
Update frequency
irregular
Identifier
http://data.europa.eu/89h/f4cb0c69-5d43-4765-9ec8-e79cb28c21bc
Popularity