ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data

Abstract

ViroMatch is an automated pipeline that takes metagenomic sequencing reads as input and performs iterative nucleotide and translated nucleotide mapping to identify viral sequences. We provide a Docker image for ViroMatch, so that users will not have to install dependencies.

A Case of Persistent Human Pegivirus Infection in Two Separate Pregnancies of a Woman

“…Nucleic acid isolated from samples with Quick DNA/RNA Viral Kit (Zymo Research, # D7020) was used was used as input for the ViroCap assay [ 31 ]. Viral sequences were analyzed with the ViroMatch pipeline [ 33 ]. After identifying HPgV sequences in the two maternal samples, HPgV genomes were assembled with IDBA-UD [ 34 ] and contigs were extended with PRICE software [ 35 ].…”

Comparison of Metagenomic Sequencing and the NanoString nCounter Analysis System for the Characterization of Bacterial and Viral Communities in Vaginal Samples

“…The libraries were sequenced on the Illumina (San Diego, CA) NovaSeq instrument. The data were analyzed to characterize the eukaryotic virome as previously described ( 1 , 23 ). Bacterial communities were analyzed with KRAKEN2 ( 24 ), using the Bacteria database, which is comprised of the complete bacterial genomes in the NCBI RefSeq database, which we further supplemented with draft genomes from taxa that were not represented in RefSeq but were important for the characterization of the vaginal microbiome: Atopobium , Megasphaera , Prevotella , and Lactobacillus iners .…”

Association of the human semen DNA virome with successful in vitro fertilization

“…The enriched libraries were sequenced on the Illumina NovaSeq (Illumina, Inc., San Diego, CA). The sequencing data were analyzed using the ViroMatch Pipeline (13). Viral sequences of interest were reviewed manually using NCBI BLAST to confirm viral subtypes (14).…”