Releases: mhammell-laboratory/TEsmall
Releases · mhammell-laboratory/TEsmall
Version 2.0.8
Major change
- Disabled EM component of TEsmall due to potential overcounting
- Thanks to @NavandarM for reporting the issue
Minor change
- Updated HTML output to include annotated reads from 3' tRF analysis
Version 2.0.6
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
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.
- Enables user to create their own reference genome (e.g. into
Version 2.0.4
Minor changes
- Added compatibility to Bokeh version 3 or higher
- replacing
plot_width
andplot_height
withwidth
andheight
respectively.
- replacing
Version 2.0.3
Minor changes
- Changed output file names to better describe their contents.
Version 2.0.2
Improvements
- Added support for Bowtie large indices (e.g. GRCz11)
Version 2.0.1
Bug fix
- Removed duplicated tRNA entries in count summary output (#12)
- Thanks to @sanatbhadsavle for identifying the bug.
Version 2.0.0
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
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