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Command-line execution

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

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Command-line execution

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  1. BASH script Command-line execution -B -F Add BED file to ideograms Rename/Select bam files Filter by mapping quality / duplicates -q / -d -c -b Calculate coverage Parse data for directional information Generate UCSC-format BED Build genome? YES NO Call fragment templates based on W:C ratio Generate plotting parameters -A 2 -a R scripts SCE? YES -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 Orphan fragments? YES -A 1 Estimate template based on read numbers NO Plot Heatmap Fragment BED file Plot unknown fragments SCE & mis-orient BED files Print Summary pdf Plot ideograms

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