PBSuite Blog

Software for Long-Read Sequencing Data from PacBio

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PBSuite 15.8.24

Below is a quick rundown of the changes we've made to PBSuite.
The most important of which is about the single 5' end contig extension correction in PBJelly. It's important to rerun your genome upgrade with the new version if you had any significant number of single end extensions.
Otherwise, most of the changes were weird edge-cases that were fixed thanks to you, the active user community, giving much needed feedback.

PBHoney has also officially started participating in the Genome in a Bottle project hosted by NIST. Part of this work for us here at PBSuite will be to identify ways in which we can improve PBHoney. With only a little bit of work thus far, we've begun spit-balling and testing new ideas. So, be on the lookout for new versions and details.

--
~/Adam English

CHANGELOG

    Removed old executables:
      MakeOverlapTable.py
      MakeReciprocal.py
      Polish.py
      OLCAssembly.py
      chunkyBlasr.py

    Added --reportContigs to spots so that you can see the contig created
    that called your spot if you want. By default it's off.

    Added downsampling to Honey.py asm instead of failing when too many
    reads were present. - and only for Illumina reads

    Added new parameters for minimum gap inflation size for Jelly

    Fixed an error where we weren't correctly using the -sa index for
    Jelly mapping across all jobs

    Corrected an error where single extend from 5' end captured gap
    filling wasn't having the consensus bases correctly placed

    Fixed a pysam cfaidx exception caused by SVs in Honey spots being
    discovered within --buffer distance of reference start thus raising
    an IndexError:start out of range(<some negative number>)

Posted by 2015-09-01