The clc_adapter_trim Program

Trims adapters from sequences.

Many sequencing technologies may leave whole or partial adapter or linker sequences in the reads for various reasons. The clc_adapter_trim program is used to find and remove such adapters from the reads.

The clc_adapter_trim tool identifies likely adapters in reads and removes them. To account for sequencing errors known adapter sequence are aligned with each read. Matching positions in these alignments score 1, while each mismatch costs 2 and each gap costs 3. By default, a region that aligns with a score of at least 10 is considered a possible adapter region. The -c option can be used to change the default score threshold of 10.

By default, the clc_adapter_trim tool trims bases towards the 3´ end of reads using the following approach:

With the -e option it is possible to change the behavior so the reads are trimmed towards the 5´ end of reads, rather than the 3´ end. In this case, the conditions described above are the same, with the directionality of the actions reversed.

The clc_adapter_trim program allows fine control over the behavior of the tool. For example,

For adapter sequences given with the -a, -j or -k options, the reverse complement of the adapter sequences is automatically added to the list of adapters to search for.

Further details can be found in Options for All Programs.