Installation: This requires: samtools-0.1.18+, and blasr 1.MC.rc39+ (github.com/mchaisso/blasr). Running: Usage: screenInversions sam genome output -j (int) Use n cores. -f Sam is fofn of sam files. -w (int) Expand reference by window. -r Allow reverse complement. -d Make dotplot -k (int) Use k for matching ( k <= 15). --noClip Do not clip The typical usage for screening ~50kbp assembled contigs is: samtools view reads.bam | \ screenInversions /dev/stdin genome.fasta inversions.table \ -w 5000 \ -r \ --noClip \ -j 8 The output should be merged: bedtools sort -i inversions.table | bedtools merge -n