In the past I have used the Sanger data analysis tool to check sequencing results, but I find the new version "Map reads to reference.." gives an error "Subtask {Compose alignment} is failed: No read satisfy minimum identity criteria." even for reads that aligned in the past, or have 97% identity when aligned with blastn.  Any idea what could be the problem?

Hi! We're sorry for your bad experience! And we would be very grateful, if you send us the data (e.g. by e-mail), so we can reproduce the issue locally.

Meanwhile, would you like me to give you a link to the previous UGENE version? Do you use Windows OS?

Can you tell me which email I can send too?

Thanks

Please send them to ugene@unipro.ru.

Thanks for the data!
Note that we updated the algorithm for mapping Sanger reads in UGENE 1.28. We've checked it with the data you sent and the read has been mapped successfully.

The new version 1.28 will be released at the beginning of the next week. We appreciate if you check the new algorithm and inform us, if everything is fine.

Thanks it is working now.  Like the new viewer, nice that it shows orientation of the mapped read.

Thanks for informing and sharing with us your opinion about the viewer.
If you have any additions to your feedback in future, you're also welcome to share it.

I may have spoken too soon - while some reads are now aligning properly, others that align well via online blastn still do not map using ugene.  I have sent test data in another email.

Thanks!

Thanks! We'll look into this as well. We'll inform you about the result in the nearest future.

Hello again!

Please note that "Mapping min quality" parameter in the "Map Sanger Reads to Reference" has another meaning than the "Identity" value of a BLAST pairwise alignment:
* The first one specifies identity between the whole read and the corresponding region of the reference sequence.
* The second one specified identity between the aligned part of the read and the corresponding region of the reference sequence.

However, we found out that there were indeed a bug in the filtering by identity. See UGENE-5863 for details.

Thank you again for the report and the data. The issue will be fixed in UGENE 1.28.1 that will come out soon.

UGENE 1.28.1 has been released recently. The issue is fixed.

Note that the "Identity" parameter in the dialog was replaced by "Silmilarity" as the mapping algorithm takes into account gaps when comparing reference and read. See the "Mapping Reads to Reference" chapter in the documentation for details.

Your feedback about the new UGENE version is welcome.