From: Pairwise comparative analysis of six haplotype assembly methods based on users’ experience
Method | Model or algorithms | Assumptions | Seq Error | Seq Cov | Read Len | Obj Fun |
---|---|---|---|---|---|---|
HapCUT2 | maximum likelihood-based | Heterozygous sites known in advance; allele count independent | X | X | X | |
MixSIH | probabilistic mixture model | sequence error rate independent of fragments and positions; mixture probabilities are equal (pm(0) = pm(1) = 0.5 ) | X | X | X | |
PEATH | probabilistic evolutionary algorithm | All input variables are independent, no copy number variation | X | X | ||
WhatsHap | Fixed-parameter tractable algorithm, dynamic programming | Allele with higher alignment score is assumed to be supported by the read, variants are sorted by position, recombination events equally likely at any position | X | X | X | |
SDhaP | MEC | X | X | X | ||
MAtCHap | maximum allele co-occurrence | X | X |