Clostridium thermocellum DSM 1313 LL1010 resequencing
Genomic DNA was submitted to the Joint Genome Institute (JGI) for sequencing with an Illumina MiSeq instrument.  Unamplified libraries were generated using a modified version of Illuminas standard protocol. 100 ng of DNA was sheared to 500 bp using a focused ultrasonicator (Covaris). The sheared DNA fragments were size-selected using SPRI beads (Beckman Coulter). The selected fragments were then end-repaired, A-tailed, and ligated to Illumina compatible adapters (IDT, Inc.) using KAPA- Illumina library creation kit (KAPA biosystems). Libraries were quantified using KAPA Biosystems next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified libraries were then multiplexed into pools for sequencing. The pools were loaded and sequenced on the Illumina MiSeq sequencing platform utilizing a MiSeq Reagent Kit v2 (300 cycle) following a 2 × 150 indexed run recipe.  Paired-end reads were generated, with an average read length of 150 bp and paired distance of 500 bp.