Hello everyone,

thanks for your time.

Regarding Hisat2 Genome based indexing:

I was trying to understand the indexing part in different aligners, i understood bowtie2 and bwa versions, built with (BWT, SA, FM index).

I tried a lot to understand the graph based indexing but couldn't reach to the level to understand the GFM index, i need some suggestions and help to understand how did they build the graph and what does it mean by "Prefix sort graph - doubling and pruning", how is this graph constructed. i understood how the LM mapping part after prefix sorted graph.

I'll be very thankful for your suggestions.

- How to understand prefix sorted graph which is saying doubling and pruning.

best regards, Kiran.

Hi,

I just realized that it is build based on the Finite automata theory, which is actually accepting the multiple string alignments possible.

thanks.