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Releases: mhammell-laboratory/TEsmall

Version 2.0.8

26 Nov 14:23
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Major change

  • Disabled EM component of TEsmall due to potential overcounting

Minor change

  • Updated HTML output to include annotated reads from 3' tRF analysis

Version 2.0.6

12 Nov 14:43
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Major change

  • Added support for Docker/Singularity

Bug fix

  • Fixed 3' TRF module to prevent downstream steps from prematurely terminating generation of 3' TRF-free BAM file
    • Credit to Alice Godden for identifying the bug

Version 2.0.5

06 Oct 20:30
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Major change

  • Remove reference genome choice in command line argument.
    • Enables user to create their own reference genome (e.g. into $HOME/TEsmall_db/genomes/)
    • Error now thrown if the reference genome is not installed by user and not available for download.

Version 2.0.4

06 Oct 19:19
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Minor changes

  • Added compatibility to Bokeh version 3 or higher
    • replacing plot_width and plot_height with width and height respectively.

Version 2.0.3

31 Mar 15:46
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Minor changes

  • Changed output file names to better describe their contents.

Version 2.0.2

17 Feb 17:35
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Improvements

  • Added support for Bowtie large indices (e.g. GRCz11)

Version 2.0.1

27 Jul 20:14
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Bug fix

  • Removed duplicated tRNA entries in count summary output (#12)

Version 2.0.0

14 Jun 19:05
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Major changes

  • Implementation of EM algorithm in quantification of multi-aligners
  • Added workflow to identify tRNA fragments (tRFs)
  • Added mm39 genome build.
  • Support for mm9 and dm3 genome builds discontinued.
    • Please use previous releases for these genomes.

Many thanks to Kat O'Neill (@ksoneill) for the implementation of the various updates in this release.

Version 1.0.0

12 Jul 11:57
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Major changes

  • Python 3 compatibility (Credit to @stela2502 for the help)
  • Updated plotting to be compatible with newer Bokeh libraries (version 1.x and 2.x) (Resolving an issue raised in #5)
  • Can specify different folder containing TEsmall databases (defaults to $HOME/TEsmall_db if not specified)

Minor changes

  • Renamed tool to TEsmall
  • Added dm6, hg38 and mm10 genomes for download