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6. A ZKV, CHIKV and YFV Dataset

Inês Mendes edited this page Aug 9, 2019 · 2 revisions

We've exhibited the analysis results of selected HTS data derived from DENV-positive samples. While working with metagenomic samples, it's import ensure that datasets containing other Flavivirus other than DENV, such as Zika (ZKV), Chikungunya visrus (CHIKV) and Yellow Fever virus (YFV), produce no false positive results.

To evaluate DEN-IM's specificity, we've analysed with DEN-IM a datasets containing a collection of 41 samples, obtained from SRA, containing sequences of CHIKV, YFV and ZKV (11 CHIKV, 16 ZKV and 14 YFV) from targeted and amplicon metagenomics studies.

Data

Run ID Bioproject SRA Study Source Organism
SRR8031152 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8062732 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8031153 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8063606 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8063603 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8063605 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8031155 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8031154 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8063604 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR8062733 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR7985391 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR7985394 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR7985620 PRJNA494391 SRP163225 Shotgun Metagenomic CHIKV
SRR7985390 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR7985392 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR7985621 PRJNA494391 SRP163225 Shotgun Metagenomic CHIKV
SRR5179639 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179637 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179646 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR7985389 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR7985622 PRJNA494391 SRP163225 Shotgun Metagenomic CHIKV
SRR7985619 PRJNA494391 SRP163225 Shotgun Metagenomic CHIKV
SRR5179667 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179653 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR7985393 PRJNA494391 SRP163225 Shotgun Metagenomic ZKV
SRR5179638 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179636 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179666 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179650 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179649 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179643 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179635 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179645 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179642 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179644 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179647 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179641 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179640 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179652 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179648 PRJNA361543 SRP096859 Amplicon Metagenomics YFV
SRR5179651 PRJNA361543 SRP096859 Amplicon Metagenomics YFV

Using the GetSeqENA tool, the raq sequencing data of the shotgun metagenomics dataset can be downloaded and stored in a folder named fastq/.

Analysis

DEN-IM was executed with the raw sequencing data using the default parameters and resources in a laptop qith 8 CUPS and 8GB of RAM. All these samples failed DEN-IM’s workflow, 11 due to not enough sequenceing data remaining after quality trimming, and the remaining 30 due to very low estimated coverage of the DENV genome, as expected. The results for this analysis are available online.

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