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Viral metagenomics from mammalian feces (Sciuridae)

Subcategory: molecular
Standard reference: Steel et al. (7)
Papers: 2 | Mentions: 2

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Description

A comprehensive protocol for extracting, amplifying, sequencing and analyzing viral DNA from fecal samples to identify microviral genomes. Uses rolling circle amplification followed by high-throughput sequencing and bioinformatic analysis.

Typical Equipment

  • High Pure viral nucleic acid kit
  • TempliPhi 2000 kit
  • Nextera DNA library preparation kit
  • Illumina HiSeq 4000 sequencer
  • Trimmomatic v0.39
  • metaSPAdes v3.12.0
  • VirSorter
  • RASTtk
  • BLASTp
  • BBMap

Output Measurements

  • microvirus genome sequences
  • genome size
  • GC content
  • gene annotations

Papers Using This Protocol (2)

article

Microvirus Genomes Identified in Fecal Samples from Yellow - Bellied Marmots

2022Microbiology Resource Announcementsusing
article

Diverse cressdnaviruses and an anellovirus identified in the fecal samples of yellow-bellied marmots

2021Virologyusing