search

seqan / iGenVar

The official repository for the iGenVar project.
BSD 3-Clause "New" or "Revised" License
9 stars 8 forks source link

Re-assemble reads to the reference genome and determine haplotypes #154

Open joergi-w opened 3 years ago

joergi-w commented 3 years ago

For an active region:

Create an assembly graph with the reference as template. Take each read and match it to graph segments. Add new nodes if a part does not match. Keep track how many reads support each path segment and determine the most likely paths. Build haplotype sequences from likely paths.

joergi-w commented 3 years ago

Use T-Coffee or parts of SViper for implementing this? (both SeqAn2)