Additional file 1: Table S1. of SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads

Spoligotype prediction and time performance of 161 Mtb isolates with SpoTyping in comparison with SpolPred. Table S2. Spoligotypes of 14 Mtb isolates determined from contigs obtained by de novo assembly, Velvet. Table S3. Actual length at different percentiles used as the read length for SpolPred spoligotype prediction of isolates sequenced on Illumina MiSeq. Table S4. Spoligotype prediction for Mtb isolates sequenced by Illumina MiSeq with SpoTyping in comparison with SpolPred. Table S5. Actual length at different percentiles used as the read length for SpolPred spoligotype prediction of isolates sequenced on Ion Torrent. Table S6. Spoligotype prediction for Mtb isolates sequenced by Ion Torrent with SpoTyping in comparison with SpolPred. Table S7. Statistics of time and accuracy of running SpoTyping on 50 iterations each for various down-sampling ratios of an H37Ra Mtb isolate. Table S8. Statistics of time and accuracy of running SpoTyping on 50 iterations each for various down-sampling ratios of a Beijing Mtb isolate. Table S9. Lineages of 14 discordant Mtb isolates by SpoTyping, experimentally reported and phylogenetic tree. (XLSX 55 kb

Additional file 1: Table S1. of In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer

Informative RD for MTC analysis and its characteristics. (XLS 25 kb

Additional file 4: Table S4. of In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer

Outputs from RD-Analyzer in the validation set of Mtb isolates. (XLS 107 kb

Additional file 1: of Local transmission and global dissemination of New Delhi Metallo-Beta-Lactamase (NDM): a whole genome analysis

Figure S1. Read depths along the reference plasmid sequences based on Illumina MiSeq sequencing reads mapping. Figure S2. Whole-genome Neighbor-Joining tree of local bla NDM-positive bacteria. Figure S3. In vitro trans-conjugation assay of local bla NDM-positive isolates. Figure S4. Details of the bla NDM-positive plasmid clusters. Figure S5. SNP-based refinement maximum likelihood trees of bla NDM plasmid clusters. Figure S6. SNP-based refinement Neighbor-Joining trees of bla NDM plasmid clusters. Figure S7. Investigation of transposition events among bla NDM plasmid clusters by recombination analysis. Table S1. Summary of Illumina sequencing and de novo assembly statistics. Table S2. Descriptive statistics for plasmid mapping. Table S3. Names and accession numbers of bla NDM-positive plasmids. Table S4. Result summary of recombination analysis. (DOCX 2781 kb