What it does
This tool creates a fragment recruitment plot from a SAM input file. Its main purpose is to display a graph of aligned metagenomic reads against an organism's reference genome. The percent identity is calculated based on the MD: tag in the optional form field of the SAM format.
Input Datasets/Files
Two input types are required in this tool:
If using Bowtie2 output, follow these steps to format the file properly:
Filter the BAM/SAM output from Bowtie2 by executing the "samtool_filter2" tool from the Tool Shed. More information can be found in this link: http://toolshed.g2.bx.psu.edu/view/devteam/samtool_filter2
TIP: This ensures the file contains all aligned reads without any missing MD tags per line.
Convert BAM-to-SAM by using using the tool "bam_to_sam" installed from the Tool Shed. Additional information can be found in this link:: http://toolshed.g2.bx.psu.edu/view/devteam/bam_to_sam
Output Example
An example image (png format) of a fragment recruitment plot.