Genome sequence of Lactobacillus crispatus LC31
For genome assembly, low quality PacBio subreads (length <1 kb) were removed by filtering and the remaining reads were self-corrected by Pbdagcon (https://github.com/PacificBiosciences/pbdagcon). Corrected reads were used for de novo assembly with Celera Assembler version 8.3 [12]. Single-base corrections were made with GATK and SOAP tool packages (SOAP2, SOAPsnp, SOAPindel) [13, 14]. To trace the presence of any plasmid, the Illumina reads were filtered and mapped to the bacterial plasmid database (http://www.ebi.ac.uk/genomes/plasmid.html, last accessed July 8, 2016) using SOAP.