Draft Whole-Genome Sequence of Xenorhabdus nematophila strain SC 0516 associated with entomopathogenic nematodes host Steinernema carpocapsae
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.