Read types support

[mictadlo]

Hi,
Does Flash2 support real Illumina mate-pair reads or just paired-end reads?

Thank you in advance.

Michal

[msettles]

If by "mate-pair" you mean long-insert libraries, then on. The --allow-outies in the original flash algorithm is intended for use with long-insert libraries ("mate-pairs"). We've used the same algorithm and flag --allow-outies to identify and remove adapter in paired-end reads. Have not used it for mate-pairs, but intuitively it would seem to have the opposite of desired effect and cut off all the useful sequence leaving the mate-pair linking adapter.