LMIC human fecal stool sample CAM001666-008132, whole-genome shotgun sequencing
Genomic libraries were prepared using Illumina DNA Prep Tagmentation kit         (Illumina, San Diego, CA), following the manufacturers instructions except for changes that         increased library insert size to a median about 600 bp. Libraries had a final elution of 10         l Illumina resuspension buffer. Illumina-DNA/RNA UD Indexes Plate A, B, C and D dual index         adapters were ordered from Integrated DNA Technologies (Coralville, IA) and used at 1 M         final concentration. Instead of pooling equal volume, individual libraries were quantified         using the KAPA Library Quantification Kit (Roche). Libraries were quantified in 10 l volume         reactions and 90-s annealing/extension PCR, and then pooled and normalized to 4nM. Pooled         libraries were re-quantified by ddPCR on a QX200 system (Bio-Rad, Hercules, CA), using the         Illumina TruSeq ddPCR Library Quantification Kit and following the manufacturers protocols.         Libraries were sequenced using a 2 x 250 bp paired end v2 reagent kit on a MiSeq instrument         (Illumina) at 16 pM, following the manufacturers protocols.