A schematic flowchart for processing of paired-end sequences with MGmapper.

<p>MGmapper processes fastq reads in four steps. These consist of: (I) Trimming and mapping reads against a phiX bacteriophage to remove potential positive control reads. (II) Mapping to specified reference databases, post-processing of BWA-mem alignments to remove reads with low alignment score or insufficient alignment coverage. (III) Identification of best hits in <i>bestmode</i>: Assignment of a read-pairs to only one specific reference sequence based on the highest sum of alignment scores. In <i>fullmode</i>, assigned a read-pair to a reference sequence even if a higher alignment score is found when mapping to another reference sequence database. This will provide best target match, considering only the sequences present in one particular reference database. (IV) Compilation of abundance statistics, read and nucleotide counts, depth, coverage, and summary reports.