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Bookend v1.1.0: ONT update
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@maschon0 maschon0 released this 20 Apr 11:11
· 11 commits to master since this release
v1.1.0
ffc6c35

Bookend update to implement a number of improvements, including easier handling of Oxford Nanopore (ONT) reads.

CHANGES:

  • bookend elr: a number of --data_type presets were added for "pacbio", "ont", "direct_rna", and "smartseq" libraries, and it will attempt to adjust settings appropriately to recognize the strand orientation and end labels for each data type.
  • bookend elr: if cDNA reads are used without trimming end labels, the argument --untrimmed allows correct inference of RNA strand from the sequence composition of the softclipped ends of each alignment. Use for ONT Direct cDNA and PCR cDNA data if it was not pre-processed with bookend label.
  • bookend elr: added the choice to provide a set of reference splice junctions with either --reference (GTF/GFF3/BED12) or --splice (BED6/SJ.out.tab). This prevents noncanonical reference junctions from being discarded.
  • bookend assemble: can now recognize a sorted aligned long-read BAM file and attempts a "simple assembly". NOT recommended as a default, but useful for a quick look at whether Bookend will work with the provided alignments. For recommendations on how to properly process ONT/PacBio reads, see the updated Bookend User Guide
  • bookend assemble: added a --truncation_filter so that the aggressiveness of filtering putative RNA degradation artifacts can be user specified.
  • bookend fasta: added the option --orf to report the longest open reading frame translation as an amino acid FASTA file for an assembly/annotation.

BUGFIXES:

  • More efficient pruning of low-abundance splice junctions during Membership Matrix construction
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