Arachne provides a number of fasta files containing undesirable sequence which is looked for in the reads. Reads are aligned to these sequences, and matching portions of the read are trimmed. If the trimming results in a read with less than 50 bp, the read is marked as deleted, and its length is set to 0. This is called Blast trimming.
The following files are included in the Arachne download and can be modified or removed according to the needs of the user:
- contains an extensive library of full-length vector sequences.
- gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
- contains a library of E. coli tranposable elements.