title: gDNA-Seq of Mycobacterium tuberculosis
design: Genomic DNA of an XDR-TB isolate from Nepal, NP1701X, was sequenced using an Illumina MiSeq instrument. Paired-end reads were mapped to the publicly-available annotated genome of M. tuberculosis reference strain H37Rv (accession number NC_000962.3) by Burrows-Wheeler Alignment. Variants relative to the H37Rv reference genome were called and variant annotation was performed using Geneious Prime 2019.2.3 (https://www.geneious.com). A draft genome assembly of contigs (500bp) was assembled de novo using the SPAdes assembler (v3.7). Assembled contigs were ordered with respect to the M. tuberculosis H37Rv genome using ABACAS.