Viruses in metagenomes (coming soon)

Detection and quantification of viruses in short-read shotgun metagenomic sequences. The client provides raw shotgun metagenomic sequences and sample metadata.

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This analysis starts with raw short-read Illumina metagenomic sequences, which are provided by the client and typically obtained from a sequencing service provider. We deliver a summary report and key data products for presentations and downstream investigations.

Main steps and deliverables:

• Basic quality filtering and trimming of sequences to improve overall data quality.
• Assembly of reads into contiguous sequences (contigs).
• Detection of viral contigs using MetaPhinder, VirSorter or viralVerify, depending on user preference.
• Estimation of completeness of viral contigs.
• Quantification and visualization of viral abundances across samples.

In addition, we also provide a thorough Materials & Methods writeup for use in your publications.

• Short-read DNA sequences from an Illumina next-generation sequencing platform or similar. Sequences must be provided as demultiplexed fastq files, one file per sample and per read direction. For paired-end reads, you will thus need to provide two fastq files per sample.
• Metadata for all samples, in the form of a table file (e.g., CSV or Excel). This table must at the very least specify sample IDs.

Main databases and software used in this analysis:

• MetaPhinder
• VirSorter2
• CheckV
• metaViralSpades
• viralVerify

• Schackart, K. E., Graham, J. B., Ponsero, A. J., Hurwitz, B. L. (2023). Evaluation of computational phage detection tools for metagenomic datasets. Frontiers in Microbiology 14:1078760

Price starts at $50 base + $5 per sample. Final price may differ depending on user settings, and will be available prior to order submission. Log in to see availability and payment modalities.