title: Draft Whole-Genome Sequence of Xenorhabdus nematophila strain SC 0516 associated with entomopathogenic nematodes host Steinernema carpocapsae
design: The reads quality was analyzed with FastQC. The Illumina adapter sequences were removed using the ILLUMINACLIP trimming step of Trimmomatic v0.39 program. Poor quality bases from Illumina paired-end reads were removed using the DynamicTrim algorithm of SolexaQA++ v3.1.7.1 software package with Phred quality score Q=13. The paired-end reads were de novo assembled using the SPAdes v3.14.1 program with the following options: i) only runs assembly module (--only-asembler); ii) reduce the number of mismatches (--careful); and iii) k-mer lengths between 21 to 71 that generated 248 contigs. Contigs with length less than 500 bp were discarded and the remaining ones used for a multi-draft-based analysis using the genome of Xenorhabdus nematophila strain YL001 through MeDuSa v1.6 scaffolder. A final assembly polishing step was performed by remapping the quality-filtered sequence reads on the ordered scaffolds using BWA and passing the resulting sorted binary alignments to SAMtools for indexing. The indexed alignments were used by Pilon v1.23.