Computational protocol: Molecular Identification of Bacteria in Tracheal Aspirate Fluid from Mechanically Ventilated Preterm Infants

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Protocol publication

[…] Sequence data (fasta and quality files) were assigned to samples by bar code and screened for low level quality defects (short sequences <150 nt in length, >1 sequence ambiguity, best read with quality ≥20 over a 10 nt moving window) by the software program BARTAB . Non-bacterial sequences were removed from the dataset by requiring a close match with a bacterial secondary structure rRNA model within Infernal . Sequences identified as potential chimeras by ChimeraSlayer were also removed from the dataset. Taxonomic assignment was done by the Ribosomal Database Project Classifier software . We used a BLAST database containing bacterial isolates identified in the Silva ARB database (version 104) to assign species names . The taxonomic information was used to construct sequence groups with identical taxonomic rank, which were used to calculate ecology statistics for each sample. Shannon diversity and Chao1 were computed, using rarefaction (100 replicates) to compensate for differences in number of sequences per sample, using the biodiv functionality contained within the XplorSeq Toolkit , . […]

Pipeline specifications

Software tools XSTK, ChimeraSlayer, RDP Classifier
Application 16S rRNA-seq analysis
Organisms Homo sapiens
Diseases Bronchopulmonary Dysplasia, Chorioamnionitis, Escherichia coli Infections