Vector trimming is a pre-processing step in which bits of vector sequence are removed from input reads. After sequencing and base-calling, there can still be a bit of vector (i.e. a part of the genome from the bacteria used for cloning) at the beginning of a read. Vector trimming looks for this sequence and removes it before using the read for Whole Genome Assembly.
There are two methods of vector trimming:
- Exact trimming looks in each read for the cloning site of the particular vector used in sequencing that read.
- Blast trimming aligns each read to a selection of potential contaminants, including a wide array of vector sequences.
The vector sequences are contained in the following input locations: