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Update faq.rst
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skoren authored Dec 16, 2018
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Expand Up @@ -125,22 +125,22 @@ What parameters should I use for my reads?
contiguous assemblies on large genomes.

**Nanopore R9 2D** and **PacBio P6**
Slightly decrease the maximum allowed difference in overlaps from the default of 14.4% to 12.0%
with ``correctedErrorRate=0.120``
Slightly decrease the maximum allowed difference in overlaps from the default of 12% to 10.5%
with ``correctedErrorRate=0.105``

**PacBio Sequel**
**PacBio Sequel V2**
Based on an *A. thaliana* `dataset
<http://www.pacb.com/blog/sequel-system-data-release-arabidopsis-dataset-genome-assembly/>`_,
and a few more recent mammalian genomes, slightly increase the maximum allowed difference from the default of 4.5% to 8.5% with
``correctedErrorRate=0.085 corMhapSensitivity=normal``.
Only add the second parameter (``corMhapSensivity=normal``) if you have >50x coverage.

**PacBio Sequel V3**
The defaults for PacBio should work on this data.

**Nanopore R9 large genomes**
Due to some systematic errors, the identity estimate used by Canu for correction can be an
over-estimate of true error, inflating runtime. For recent large genomes (>1gbp) with more
than 30x coverage, we've used ``'corMhapOptions=--threshold 0.8 --num-hashes
512 --ordered-sketch-size 1000 --ordered-kmer-size 14'``. This is not needed for below 30x
coverage.
over-estimate of true error, inflating runtime and disk usage. The newest releases should automatically adjust for this but if you are using Canu 1.6 or older you can try ``'corMhapOptions=--threshold 0.8 --ordered-sketch-size 1000 --ordered-kmer-size 14'``.


Can I assemble RNA sequence data?
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