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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

Fig. 1

Workflows implemented in the ags.sh and acn.sh tools. a ags.sh workflow consists of the following steps: 1) Filtering out and trimming reads to obtain an appropriate read length range using the BBduk tool [29] (optional step); 2) Predicting the Open Reading Frames (ORFs) with FragGeneScan-plus [30] (optional step); 3) Annotating the single-copy genes in the ORF’s amino acid sequences with UProC [32]; 4) Computing the Number of Genomes (NGs) as the mean gene coverage of the single-copy genes; 5) Counting the total number of base pairs; 6) Computing the Average Genome Size (AGS) as the ratio of the total number of base pairs to the NGs. b The tasks performed by acn.sh are as follows: 1) Annotating the 16S rRNA genes with SortMeRNA [34]; 2) Computing the 16S rRNA gene coverage as the number of annotated base pairs divided by the 16S rRNA gene length; 3) Parsing the NGs from the ags.sh output; 4) Computing the ratio of the 16S rRNA gene coverage to the NGs to derive the 16S rRNA gene Average Copy Number (ACN)

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