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KGEM (Top down approach) v0.20 Basic functionality:

Read file with aligned reads (.sam). Initialize population as random sample of fixed size from this reads.

Sequentially repeat KGEM steps until convergence:

1. Rounding
2. Frequency estimation (FEM)
3. Allele frequency estimation (KGEM)

Output corrected haplotypes in fasta format.

New features v0.20

• KGEM derandomized with maximization of hamming distance between seeds
• Monte Carlo parameters dropped.
• Threshold changed to min hamming distance between seeds
• Loop overflow condition added (get rid of infinite loops)

features v0.10:

• KGEM steps include threshold clean step: Drop all genotypes with frequency less than threshold level (Default 0.05%)

• Monte Carlo series of experiments support implemented: Run the whole procedure n times and select haplotypes which appeared at least m times (Default n:4, m:3)

example of usage:

java -jar KGEM.jar reads.sam -k 50 -tr 5