Generate your own duplicated window record file:

It is highly recommended to generate the corresponding file for each chromosome separately and then concatenate the output files in the correct order.

Step 1: Split genome into short kmer sequences.

 python 0.1.Kmer_Generate.py [OPTIONS] FAFILE WINSIZE OUTFILE

 Required arguments
 <FAFILE> Reference sequence in FASTA format
 <WINSIZE> The size of the window to use for CNV calling
 <OUTFILE> Output kmer file in FASTA format
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 Example: python 0.1.Kmer_Generate.py reference.fa 800 kmer.fa

Step 2: Align the kmer FASTA (from step 1) to reference genome using blasr.

 Example: blasr kmer.fa reference.fa --sa reference.fa.sa --out kmer.aln -m 5 --noSplitSubreads --minMatch 15 --maxMatch 20 --advanceHalf --advanceExactMatches 10 --fastMaxInterval --fastSDP --aggressiveIntervalCut --bestn 10

Step 3: Generate duplicated window record file.

 python 0.2.Kmer_Link.py [OPTIONS] BLASR WINSIZE OUTFILE

 Required arguments
 <BLASR> blasr results (-m 5 format)
 <WINSIZE> The size of the window to use for CNV calling
 <OUTFILE> Output genome duplicated window record file
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 Example: python 0.2.Kmer_Link.py kmer.aln 800 window.link