Vector trimming

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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:

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