Cluster generation kit ver 4

Bacterial 1 kb insert DNA libraries (Purified Neochlamydia S13 and Protochlamydia R18) were prepared using a genomic DNA Sample Prep Kit (Illumina, San Diego, CA). DNA clusters were generated on a slide using a Cluster Generation Kit (ver. 4) on an Illumina Cluster Station, according to the manufacturer's instructions. Sequencing runs for 81-mer paired-end sequence were performed using an Illumina Genome Analyzer IIx (GA IIx). The 81-mer paired-end reads were assembled (parameters k64, n51, c32.1373) using ABySS-pe v1.2.0 [50] (link). Annotation of genes from the draft genome sequences was performed using Rapid Annotation using Subsystem Technology (RAST: http://rast.nmpdr.org/) [51] (link) with a local manual BLASTp search. Metabolic pathway modules were predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG: http://www.genome.jp/kegg/) [52] (link). Genome comparison was performed using RAST, and then manually visualized by GenomeMatcher 1.69 (http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html) [53] (link).

An M. massiliense strain DNA library (insert size of ∼600 bp) was prepared using the Nextera DNA Sample Prep Kit (Illumina-compatible) (EPICENTRE Biotechnologies, Madison, WI). DNA clusters were generated on a slide using the Cluster Generation Kit (ver. 4) on an Illumina Cluster Station (Illumina, San Diego, CA), according to the manufacturer's instructions. A paired-end sequencing run for 83 mers was performed using an Illumina Genome Analyzer IIx (GA IIx) with the TruSeq SBS Kit v5. Fluorescent images were analyzed using the Illumina RTA1.8/SCS2.8 base-calling pipeline to obtain FASTQ-formatted sequence data.