# HG changeset patch # User Lance Parsons # Date 1305578049 14400 # Node ID f6b94b76d16b5230b92fe303825a862631e2c8b0 # Parent 50cdd88706075656cf6e3cd0ef0afb6cca17a2df Update help diff -r 50cdd8870607 -r f6b94b76d16b cutadapt.xml --- a/cutadapt.xml Fri May 13 16:17:49 2011 -0400 +++ b/cutadapt.xml Mon May 16 16:34:09 2011 -0400 @@ -109,8 +109,6 @@ cutadapt uses a simple semi-global alignment algorithm, without any special optimizations. For speed, the algorithm is implemented as a Python extension module in calignmodule.c. -The program is sufficiently fast for my purposes, but speedups should be simple to achieve. - **Partial adapter matches** @@ -146,7 +144,7 @@ If, on the other hand, your adapter can also be ligated to the 5' end (on purpose or by accident), you should tell cutadapt so by using the *5' or 3' (Anywhere) -Adapters parameter. It will then use a different alignment algorithm and +Adapters* parameter. It will then use a different alignment algorithm and correctly trim adapters that appear in the beginning of a read. An adapter specified this way will also be found if it appears only partially in the beginning of a read. For example, these sequences