Major new release:
What has changed?
- More flexible barcode structures can now be specified: -x for each flanking sequence, -b for barcode pattern, -u for UMI pattern), where the order now matters. e.g. 10x style barcodes can be given as -x [left flank] -b [barcode pattern] -u [umi pattern] -x [right flank], but complex patterns are now allowed such as -x [left flank] -u [umi pattern] -x [middle flank] -b [barcode pattern] -x [right flank]. Flanking sequence and patterns can include wildcards "?" and IUPAC codes.
- Predefined settings for the common use cases of 10x 3' v3, 10x 3' v2, 10x 5' v2 and grep have been implemented. Requests to expand these are very welcome.
- Further development of flexiplex-filter for automatically estimating the number of cells/barcodes in an experiment and generating a short-list of barcodes.
- Note: This version is not backwards compatible and will likely break scripts developed with older versions. Importantly, the order of command line options now matters.
What has not changed?
- Performance metrics such as searching/demultiplexing sensitivity and specificity, computational speed and memory utilisation remain very similar to the previous version.