Reference Sequence Formats¶
This appendix explains the details of how breseq handles different reference sequence formats. Most importantly, this includes how different types of feature annotations are used.
Illegal Characters¶
For all sequence formats:
- In nucleotide sequences, all characters are converted to uppercase and all non [ATCG] characters are converted to [N].
- In gene names and locus tags, the characters [,;/|] are replaced with [_].
- In gene descriptions, the character [|] is replaced with [;].
Feature Annotations¶
breseq is able to more accurately predict the locations of transposon insertions if these elements are annotated in the reference genome. They must have a feature type of repeat_region or mobile_element.
