HapTree-X has ben re-release with the ability to phase linked-reads
Berger, E., Yorukoglu, D., Zhang, L. et al. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nat Commun 11, 4662 (2020). https://doi.org/10.1038/s41467-020-18320-z
It is primarily for RNA-seq based phasing but it could be worth to test as an alternative to HapCUT2. They report a much short runtime compared to HapCUT2 (10x faster!) and aslo lower switch error rate (see Table 2).
HapTree-X has ben re-release with the ability to phase linked-reads
It is primarily for RNA-seq based phasing but it could be worth to test as an alternative to HapCUT2. They report a much short runtime compared to HapCUT2 (10x faster!) and aslo lower switch error rate (see Table 2).
Github page: https://github.com/0xTCG/haptreex
Issue copied from https://github.com/FrickTobias/BLR/issues/232