Non-specific matches

In some cases it may not be possible to uniquely assign a read to a specific optimal position in a reference sequence. This for example happens when a part of a sequence is repeated a number of times among the references. A read that falls entirely within the repeat sequence is impossible to place uniquely. Using longer reads or paired sequencing alleviates the problem, but if the repeat is long enough, some reads will still be impossible to place uniquely.

The reference assembly programs allow two options for how to treat these non-specific matches: They can either be randomly placed or not placed at all. This is controlled by the -r option which has random placement as default. Since non-specific matches can always be removed later, there is usually little reason to change this option.

Supplying a value for the -t option means that you can have multiple hit positions saved in the output of the assembly. Using the clc_mapping_table program, these multiple hit positions can be retrieved from each read.