Oxford Nanopore sequencing of Agrobacterium strain LBA1190
Oxford Nanopore sequencing libraries were generated with high molecular weight genomic DNA (isolated with QIAGEN Genomic tip gravity flow columns) using the SQK-RBK004 Rapid Barcoding Kit. DNA was  pooled with another sample (S. cerevisiae DNA) before barcoding (because not enough barcodes were available). Then the barcoded sample was pooled with 11 other barcoded samples, purified with magnetic beads and loaded on the MinION. After the MinION run, the reads were first demultiplexed by barcode. Then they were headcropped (100 nt) and size selected (>500 nt). Then the filtered reads were mapped to the reference sequences. Reads mapping to Agrobacterium sequences were extracted.