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.

Adapter regions in reads may contain sequencing errors. With this in mind, the clc_adapter_trim tool identifies likely adapters by aligning the known adapter sequence 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.

Using the -c option, the default alignment score limit of 10, used as a cutoff in identifying likely adapter regions in reads, can be changed.

By default, the clc_adapter_trim tool trims bases towards the 3´f reads in this way:

With the -e option it is possible to change the behavior so the reads are trimmed towards the 5´f reads, rather than the 3´ 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,

Further details can be found in Options for All Programs.