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Our software provides an easy to use and scalable alternative to taxonomic classification of marker genes that is applicable to any nucleotide fragment.
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Additionally, our classification of markers based on contrast and height above ground resulted in four categories (above), some of which were not found in all zones.
Moreover, the evaluation and classification of markers indicated herein are based on an expert judgement of the authors, partially validated by discussions at a workshop with a wider group of experts.
After taxonomic classification of phylogenetic marker genes from metagenomic sequences in the previous step, for each taxonomic unit, we have a set of reads assigned to each phylogenetic marker gene.
Manual checking was performed to facilitate the subjective classification of individual marker assays into categories including "failed", "monomorphic", and "SNP" to ensure that only high quantity SNP calls were included in subsequent analysis.
As we have discussed in the Introduction section, estimating the abundance of taxonomic groups in a sample through the classification of phylogenetic marker genes is more accurate than that obtained through 16S rRNA analysis or classification of all of the metagenomic shotgun sequences.
Butler et al. [3] summarized a discussion of the 2007 meeting of International Society of Forensic Genetics including a classification of SNP markers based on the type of information provided by the SNP.
A pre-/post-BCG treatment classification of biological markers has been suggested [27].
The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants.
Thus, without lines that represent the nonparental derived alleles, polymorphism would not be able to be identified and this would lead to the monomorphic classification of these markers.
Selection and classification of the markers are based on the authors' expert judgement aided by discussion of an earlier version of this table with a wider group of experts.
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