SMRT analysis- what is difference between RS_HGAP_Assembly.2 vs RS_HGAP_Assembly.3

Question

[mschmid]

The title says it all: What is the difference between RS_HGAP_Assembly.2 and RS_HGAP_Assembly.3 in SMRT analysis 2.3.0?

I know that RS_HGAP_Assembly.3 is FASTER and RS_HGAP_Assembly.2 is supposed to have higher quality. But what where is the difference?

And what about the settings? So far we used RS_HGAP_Assembly.3. Can we use the same settings for RS_HGAP_Assembly.2 (for the settings which exist in both protocolls)?

Did you use both so far? Did you see big differences? If yes, what kind of differences?

Answer 1

[GenoMax]

Comparison of HGAP protocols: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-in-SMRT-Analysis

[mschmid]

Thanks! Do you already have experience how the two assembly modules differ? For RS_HGAP_Assembly.3 I always find quite some single nucleotide indel errors. How is it for RS_HGAP_Assembly.2?