Machine must have at least 64GB RAM per simultaneous instance of Virmap. Instructions for use after initial set up Using the database over gp2 is not recommended. When running Virmap, copy the database from S3 to the local instance store SSD for use. threads $(nproc) -readF /home/$USER/VirmapTest/SRR9875293_1.fastq -readR /home/$USER/VirmapTest/SRR9875293_2.fastq -useMegahit -useBbnorm -sampleName SRR9875293 -outputDir /home/$USER/VirmapTest/VirmapRun -taxaJson /scratch/VirmapDb/Taxonomy.virmap -virDmnd /scratch/VirmapDb/virDmnd.dmnd -virBbmap /scratch/VirmapDb/virBbmap -gbBlastn /scratch/VirmapDb/gbBlastn -gbBlastx /scratch/VirmapDb/gbBlastx.dmnd 2>/home/$USER/VirmapTest/VirmapRun.err Saving the installation for future use outputDir /scratch/VirmapDb Set up sra-tools configurationĮxit out of vdb-config by hitting 'x' Grab Viral mock communityįasterq-dump -t /dev/shm -e 4 -O /home/$USER/VirmapTest SRR9875293 Test run viral mock community Mkdir /scratch/tmp (if it doesn't already exist)Įxport TMPDIR=/scratch/tmp Create DB (can take > 1h)
VIR TRACKMAP UPDATE
Sudo yum -y update Download and run installer Instructions have only been tested on a fresh Amazon Linux 2 image.Įxample command line input for Amazon Linux 2: As Genbank expands, the minimum SSD and RAM requirements will expand as well. Local instance store SSD with >500 GB memory and 64GB RAM. R5d.24xlarge (recommended) or c5d.24xlarge. Installation instructions for AWS Suggested Requirements Maximal viral information recovery from sequence data using VirMAP. VirMAP offers opportunities to enhance metagenomic studies seeking to define virome-host interactions, improve biosurveillance capabilities, and strengthen molecular epidemiology reporting.Ījami, N. We validate VirMAP using published data sets and viral mock communities containing RNA and DNA viruses and bacteriophages. Here we develop VirMAP that overcomes these limitations using techniques that merge nucleotide and protein information to taxonomically classify viral reconstructions independent of genome coverage or read overlap. Viral taxonomic characterization from metagenomic data suffers from high background noise and signal crosstalk that confounds current methods. This implies the need for sensitive, specific, and practical pipelines that return precise outputs while still enabling case-specific post hoc analysis.
VIR TRACKMAP FULL
classification of the human virome is critical to a full understanding of the role viruses play in health and disease. Ω Authors contributed equally to this work. Petrosino1,2.ġ Alkek Center for Metagenomics and Microbiome Research, and 2 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas. Maximal viral information recovery from sequence data using VirMAP The paper is published at Nature Communications:
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