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. 2015 Nov 17;6:329. doi: 10.3389/fgene.2015.00329

FIGURE 1.

FIGURE 1

Scheme of the riboFrame. After QC of next generation sequencing (NGS) reads, the hmmsearch (HMMER3) is used to identify 16S ribosomal reads in both bacteria and archaea, using HMMs developed in rRNAselector (step 1). The riboTrap program then filters out incongruent assignments and de-replicate multiple assignments in order to create a set of accurate 16S reads supplemented with positional information (step 2). 16S reads are then classified using RDPclassifier to obtain a full domain to genus classification (step 3). The riboMap program eventually filters reads according to rules specified by the user, with a flexible and intuitive scheme, and performs the final rank abundance analyses (step 4). For a detailed description see the section “Materials and Methods – Description of the riboFrame Procedures.”