Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

What is happening regarding Picard tools and NovaSeq?

alecwalecw Member, Broadie

Hi,

I got picard 2.9.4 in order to get the support for CBCL files, i.e. NovaSeq output. There was a command line option 'USE_NEW_CONVERTER' added to IlluminaBasecallsToSam. Now in 2.10.0 that command-line option is gone. Also, I see some hints in the code that the functionality of ExtractIlluminaBarcodes has been folded into IlluminaBasecallsToSam. I couldn't find anything about these changes in the online documentation or the forum. Is there any documentation about these changes?

Regards, Alec

Best Answers

  • shleeshlee Cambridge admin
    Accepted Answer

    Hi @alecw,

    Yes, for CBCL handling, the v2.10.1 release does not change anything from the v2.10.0 release. I have just updated the release notes for 2.9.5, 2.10.0 and 2.10.1 at https://github.com/broadinstitute/picard/releases so you can better learn about the latest changes.

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator admin

    Hi @alecw,

    It looks like yesterday code changes were merged that remove the USE_NEW_CONVERTER argument, and release v2.10.0 reflects this change. The tool should automatically check for CBCL without having to invoke this option. Let us know if this works for you.

    You can find out about Picard release changes by skimming the release notes at https://github.com/broadinstitute/picard/releases. At this time, I've only cleaned up the release notes from v2.9.0 up to v2.9.4, so you have to do some reading-between-the-lines for the older and latest changes.

  • alecwalecw Member, Broadie

    Hi @shlee,

    I searched through all the release notes for any mention of barcode matching being folded into IlluminaBasecallsToSam and found nothing. Do I need special glasses for this reading between the lines?

    -Alec

  • shleeshlee CambridgeMember, Broadie, Moderator admin
    edited July 2017

    Hi @alecw,

    You will have to dig through the commits and the code to search for what you are looking for. Or you can wait for me to get to updating the release notes. I can be on the lookout for this ExtractIlluminaBarcodes feature you are keen on and can get back to you on any findings. The Comms team is busy prepping for an upcoming workshop (in the UK next week) and so I am unable to look into your question at this moment. I am happy to assist you thereafter.

    P.S. In the meanwhile, I'll see if I can get the developer to help.

  • alecwalecw Member, Broadie

    Thanks, @jcarey . To be completely clear, can you confirm that NovaSeq support is done (to the degree that anything is ever "done")? I.e. is there additional NovaSeq work anticipated/planned?

  • shleeshlee CambridgeMember, Broadie, Moderator admin

    I will ping @jcarey again.

  • jcareyjcarey Member, Broadie

    All anticipated work is currently done and merged to master.

  • alecwalecw Member, Broadie

    Hi @jcarey,

    Sorry to belabor this...I got 2.10.0 a few days ago. It looks like I don't need to get a newer release than that. Is that correct?

    Thanks, Alec

  • shleeshlee CambridgeMember, Broadie, Moderator admin
    Accepted Answer

    Hi @alecw,

    Yes, for CBCL handling, the v2.10.1 release does not change anything from the v2.10.0 release. I have just updated the release notes for 2.9.5, 2.10.0 and 2.10.1 at https://github.com/broadinstitute/picard/releases so you can better learn about the latest changes.

Sign In or Register to comment.