Transcript Command-line execution BASH script Add BED file to ideograms -B -F Rename/Select bam files Parse data for directional information -b Generate UCSC-format BED Build genome? NO Filter by mapping quality / duplicates -q / -d Calculate coverage Call fragment templates based on.

Command-line
execution
BASH script
Add BED file to
ideograms
-B
-F
Rename/Select bam
files
Parse data for
directional information
-b
Generate UCSC-format
BED
Build
genome?
NO
Filter by mapping
quality / duplicates
-q / -d
Calculate coverage
Call fragment templates
based on W:C ratio
-c
YES
-A 2
Generate plotting
parameters
-a
R scripts
YES
SCE?
-r
NO
Compute quality scores
Apply thresholding
Re-orient all scaffolds
Find SCE (DNAcopy)
Split into linkage groups
Find SCE interval
Read optional gap file
Call non-SCE templates
-G
YES
-A 1
Orphan
fragments?
NO
Plot
Heatmap
Fragment
BED file
Plot
unknown
fragments
SCE &
mis-orient
BED files
Estimate template based
on read numbers
Print
Summary
pdf
Plot
ideograms