PHRAP - forcelevel

Andrew G. McArthur mcarthur at
Mon Nov 8 20:45:37 EST 1999


We have been using PHRAP to assemble a 20+ Mbp shotgun sequence database

as part of the Giardia lamblia Genome Project (  We

have additionally started using it to assemble the results of some
directed sequencing on cosmid inserts.  For one cosmid of interest, we
get false assemblies when using forcelevel of 1.  When we increase the
forcelevel to 3, we get an accurate assembly.  We see similar effects
when assembling the 20+ Mbp dataset.  The online PHRAP manual leads us
to believe that forcelevel should behave in the opposite manner (text
attached below).  Does anyone have any insight on the behaviour of

Much thanks,
Andrew G. McArthur, Ph.D.
Marine Biological Laboratory
mcarthur at

---- from online PHRAP manual ----

 -forcelevel 0
 (phrap only). Relaxes stringency to varying degree during final contig
merge pass.  Allowed values are integers from 0 (most stringent) to 10
(least stringent), inclusive.

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