Hi @All.Liking Rabema, I appreciated the release of RazerS3 and the updates to the Rabema-manual (on http://www.seqan.de/projects/rabema/manual/).
Q1) So to produce a golden standard we would execute the following command (as given in step 1A):
razers3 -v -of sam -rr 100 -i 92 -m 1000000 -ds -o gold_pre.sam genome.fa reads.fq
This is however imprecisely updated, because the "-ds" option does seem to exist in razers3 ("razers3: illegal option --ds"). I assume, I can just omit the "-ds"?
Q2) In step 1b, postprocessing of the razers3-sam output is described, does that still apply?
Q3) Just a minor thing: in step (1A) you use an identity value of 92%, while you describe 6% to be the corresponding error rate in step (2). That's just a typo, I guess?!
Thanks in advance, Uwe