Fig. 1

A schematic representation of the SpoTyping workflow. If the specified input contains sequencing reads, SpoTyping first concatenates the sequencing reads to form an artificial sequence. The artificial sequence, or genetic sequences when the input contains complete genomic sequence or assembled contigs, would be built into the BLAST database. After querying the 43 spacer sequences in the database, the results are parsed to count the number of hits for each spacer sequence. A hit threshold is set to define a spacer as ‘present’ in the genome, resulting in a 43-digit binary code with 1 as present and 0 as absent, which is further translated into the octal code of the spoligotype. The SITVIT database is then queried to identify matching isolates having the same spoligotype, where the associated data of the matched isolates are downloaded and summarized as pie charts