diff --git a/documentation/source/faq.rst b/documentation/source/faq.rst index 9ba6d20ab..adb1e2f8b 100644 --- a/documentation/source/faq.rst +++ b/documentation/source/faq.rst @@ -85,7 +85,7 @@ What parameters should I use for my reads? 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. + coverage. You can also try the ``overlapper=mhap utgReAlign=true`` option which is much faster but may produce less contiguous assemblies. My assembly continuity is not good, how can I improve it? @@ -191,8 +191,8 @@ What parameters can I tweak? For low coverage: - - For less than 30X coverage, increase the alllowed difference in overlaps by a couple of percent (from 4.5% to 6.5% - (or more) with ``correctedErrorRate=0.075`` for PacBio and from 14.4% to 16% (or more) with ``correctedErrorRate=0.16`` for Nanopore), to adjust for inferior read correction. Canu + - For less than 30X coverage, increase the alllowed difference in overlaps by a few percent (from 4.5% to 8.5% + (or more) with ``correctedErrorRate=0.105`` for PacBio and from 14.4% to 16% (or more) with ``correctedErrorRate=0.16`` for Nanopore), to adjust for inferior read correction. Canu will automatically reduce ``corMinCoverage`` to zero to correct as many reads as possible. For high coverage: