Computational protocol: Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

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Protocol publication

[…] The metagenomics analysis was carried out in five steps. (1) Adapter and quality trimming as well as low complexity filtering of raw reads was performed using BBDuk of BBMap version 35.82 (http://jgi.doe.gov/data-and-tools/bbtools/). (2) Removal of human-affiliated reads from samples in a 2-step approach: i) reads that mapped against the reference genome GRCh38.p10 (GCF_000001405.36) and ii) reads that aligned to human sequences in the non-redundant nucleotide collection (nt) database from NCBI. (3) Detection of ambiguous sequences in public reference genomes and creation of curated microbial genome database that was composed of 5751 different genomes: archaea (251), bacteria (5166), fungi (225), protozoa (73), viruses (35) and the human reference GRCh38.p7 (Supplementary Table¬†). (4) Classification of reads in samples using Kraken followed by Bayesian reestimation of abundance (Bracken), and (5) Classification of reads using BLASTn of BLAST version 2.6.0. For details, see Supplementary Methods. […]

Pipeline specifications

Software tools BBTools, Kraken, Bracken, BLASTN
Databases MBGD
Application Metagenomic sequencing analysis
Organisms Homo sapiens
Diseases Cataract, Endophthalmitis