Fig. 1

Workflow for ISMapper. a Inputs are reads (fastq format) and an IS query (fasta), as well as either a reference genome to compare to or an assembly of the reads (fasta or genbank). b Reads are mapped to the IS query using BWA (dashed lines) and their pairs (i.e., flanking reads, solid lines) are retreived from the resulting SAM file using mapping flags (SAMTools). The unmapped component of soft clipped reads (solid + dashed lines), identified from the SAM file using Samblaster) are also retrieved using BioPython. c Flanking and softclipped read sequences are then mapped to either the reference genome or the read assembly (BWA), and the final mapping output is then filtered for depth to remove low coverage regions. Left and right end blocks are extracted from the resulting BAM file (using BedTools) and compared to one another to find either intersecting regions, indicating a novel IS position, or close regions, indicating a known IS position in the reference. In a novel position, overlapping sequences from the left and right ends most likely indicate the target site duplication generated during IS transposition (zoomed in section). d Results are tabulated, indicating the position and orientation of each site, whether it is novel or known, and information about the genes flanking the insertion site