How to handle PacBio simulated reads before mapping

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
20/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Stale
Domain
documentation

Research direction

The issue names no repository files or tests. Start with the pacbio2016 simulation settings and the shown minimap2 command, compare them with the nanopore2020 case, and determine whether the expected workflow needs clarification; done would be a documented, reproducible answer.

Written by the indexing model from the issue text.

Description

Hello @rrwick,
I experienced some poor mapping performance with Minimap2 for reads simulated using the pacbio2016 (only changing depth, mean sequence identity, all other settings as default). I noticed it gets progressively worse when I lower the mean sequence identity (go figure), but reads simulated with nanopore2020 models don't experience this problem.

I've been using this command to align my simulated pacbio reads

minimap2 -ax splice:hq -uf

I'm just wondering if I was meant to input my pacbio2016 reads into the Iso-seq pipeline prior to mapping with Minimap2?

Dominant language
Python
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