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author Lance Parsons <lparsons@princeton.edu>
date Mon, 16 May 2011 16:34:09 -0400
parents 8b064ea16722
children 7ed26fc9fa8a
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1:50cdd8870607 2:f6b94b76d16b
107 **Algorithm** 107 **Algorithm**
108 108
109 cutadapt uses a simple semi-global alignment algorithm, without any special optimizations. 109 cutadapt uses a simple semi-global alignment algorithm, without any special optimizations.
110 For speed, the algorithm is implemented as a Python extension module in calignmodule.c. 110 For speed, the algorithm is implemented as a Python extension module in calignmodule.c.
111 111
112 The program is sufficiently fast for my purposes, but speedups should be simple to achieve.
113
114 112
115 **Partial adapter matches** 113 **Partial adapter matches**
116 114
117 Cutadapt correctly deals with partial adapter matches. As an example, suppose 115 Cutadapt correctly deals with partial adapter matches. As an example, suppose
118 your adapter sequence is "ADAPTER" (specified via 3' Adapters parameter). 116 your adapter sequence is "ADAPTER" (specified via 3' Adapters parameter).
144 was ligated to the 3' end of the sequence. This is the correct assumption for 142 was ligated to the 3' end of the sequence. This is the correct assumption for
145 at least the SOLiD and Illumina small RNA protocols and probably others. 143 at least the SOLiD and Illumina small RNA protocols and probably others.
146 144
147 If, on the other hand, your adapter can also be ligated to the 5' end (on 145 If, on the other hand, your adapter can also be ligated to the 5' end (on
148 purpose or by accident), you should tell cutadapt so by using the *5' or 3' (Anywhere) 146 purpose or by accident), you should tell cutadapt so by using the *5' or 3' (Anywhere)
149 Adapters parameter. It will then use a different alignment algorithm and 147 Adapters* parameter. It will then use a different alignment algorithm and
150 correctly trim adapters that appear in the beginning of a read. An adapter 148 correctly trim adapters that appear in the beginning of a read. An adapter
151 specified this way will also be found if it appears only partially in the 149 specified this way will also be found if it appears only partially in the
152 beginning of a read. For example, these sequences 150 beginning of a read. For example, these sequences
153 151
154 :: 152 ::