Illumina NextSeq 500 DNA Sequencing Protocol

DNA was fragmented to 550–650 bp using a BioRuptor machine (Diagenode, Belgium). Samples were prepared following the TruSeq Nano DNA Sample Preparation Guide (Part#15041110Rev.D). Sequencing was performed using an Illumina NextSeq 500 sequencer with NextSeq Mid Output v2 Kit chemicals (Illumina Inc., San Diego, CA 92122, USA). Read- and assembly-based analyses were performed using the METAnnotatorX bioinformatic platform described below in this manuscript. Mapping of reads on nucleotide sequences was performed using the software BowTie2 [19 (link)] and retrieval of mapping or non-mapping reads was performed using the Sequence Alignment/Map tools (SAMtools) 43 [20 (link)].