6. A ZKV, CHIKV and YFV Dataset
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.
| 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/.
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.