68.5% of non-human reads aligned to nothing, possibly representing random events occurring during PCR or sequencing.
The non-human reads were mapped to the newly assembled genomes using BWA [ 33] (default parameters) and the coverage per nucleotide was determined with samtools [ 34].
Mapping the non-human reads from each isolate against the reference isolate CWL029 resulted in 93.7%-99.9% coverage of the reference genome (Table 2).
The comparative assembly of the non-human reads of the sequenced isolates against the closest available complete reference sequence among the publicly available genomes of Cpn produced between 1 and 147 contigs.
We used the comparative assembler AMOScmp-shortReads-alignmentTrimmed from the AMOS framework 3.1.0 [ 35] with default parameters for the combined mapping and de novo assembly of the remaining non-human reads.
It has been shown that mapping long sequence reads from a transcript sample against the human genome and analyzing the non-human reads has the potential of identifying non-human pathogen genes (Xu et al., 2003).
The two separate NGS files associated with this subject contained 6,858,453 and 1,343,806 reads, comprising 70%and84%4% (respectively) of all non-human reads identified at the species level in each sample.
DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads.
The remaining, non-human reads are then aligned by BLASTn (on a 64-core server) or MegaBLAST (on a laptop) to the entire NT database, using the same parameters.
The initial reads were mapped to the human genome (minimum match length 80%; mismatch allowed 10%) using HIVE hexagon [ 55] and the unaligned reads were downloaded (Additional file 1: Figures S1 and S2) and CensuScope was run to obtain the taxonomic composition of the non-human reads.
Given that many of the non-human reads can be mapped with high stringency to genomes of known pathogens, we hypothesize that this sequencing platform may be useful as a diagnostic tool for the detection of disease and that the data obtained may be used for inferring cryptic phenotypes of the sampled individuals (e.g., periodontitis status).
