Viral sequence detection and vOTU clustering

Knowledge graph centered on Viral sequence detection and vOTU clustering with 37 nodes and 129 connections. Top connected: Potentilla, Bacteria, A. tridentata, Lupinus, Veratrum.

Method synopsis

Computational pipeline using VirSorter2 and CheckV for viral sequence identification, followed by clustering into viral operational taxonomic units and taxonomic/host prediction.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem (2023), Microbiome. Implementations in other papers (listed below) may differ.

1. Sequence quality control and assembly
   Filtered reads were error-corrected using BFC (version 181) with bfc -1 -s 10 g -k 21 +10 and then assembled with metaSPAdes using the 'metagenome' flag, running the assembly module only (without error correction) and using k-mer sizes of 33, 55, 77, 99, and 127.
   Quantities: k-mer sizes: 33, 55, 77, 99, 127. Contigs ≥200 bp retained for annotationDuration: Assembly runtime varies by sample sizeConditions: Computational analysis performed on HPC systems
   Equipment: BFC version 181, metaSPAdes version 3.13.0, BBMap (https://jgi.doe.gov/data-and-tools/bbtools/)
2. Viral sequence detection
   All contigs larger than 1 kbp from individual assemblies of metagenomes and metatranscriptomes and from the combined assembly were processed with VirSorter2 (v2.0.beta) for virus sequence detection, then further refined by identifying and removing potential host contaminants using CheckV v0.8.1.
   Quantities: Contigs ≥1 kbp processed, final dataset of 9321 vOTUs after ≥50% completeness filterDuration: Computational pipeline runtimeConditions: High-performance computing environment
   Equipment: VirSorter2 (v2.0.beta), CheckV v0.8.1
3. vOTU clustering and annotation
   Predicted viral sequences were clustered into vOTUs following standard guidelines using 95% ANI and 85% AF using Mummer 4.0.0b2. Taxonomic classification was performed using geNomad v1.1.0beta and host prediction using iPHoP v0.9beta.

Typical Equipment

• VirSorter2
• CheckV
• geNomad
• iPHoP
• Mummer

Output Measurements

• viral contigs
• vOTUs
• taxonomic assignments
• host predictions

Papers Using This Protocol (1)

Species Studied With This Protocol