stringtie

This release addressed a few issues reported with the previous version, including:

• fix for cases where the --mix option was causing a segmentation fault with some data combinations
• preventing duplicate output transcripts for -e and --merge usage

• Improved sensitivity and precision for long-read assembly use cases (-L and --mix).
  • Ida Shinder (@ishinder) contributed these improvements and fixes, including a feature that uses unaligned poly(A) tails to better anchor transcript ends.
• Addressed a rare regression where very complex splice graphs in long-read bundles with high error rates prevented StringTie from completing the asse...

• fixed cases where -e option could not be used with the new -N/--nasc options
• increase floating point precision and numeric stability for calculation of coverage, FPKM and TPM values
• added a self-contained offline source package that can be built without online access
• added support for LLVM clang compilation

• Significant improvements in assembly accuracy for both short and long RNAseq reads
• StringTie can now better recognize and assemble incompletely processed (nascent) transcripts which are abundant in Total RNA libraries (e.g. Ribo-Zero data)
• Addressed -e quantification issues where some transcripts with low coverage were no longer reported in the output (fixing #238, #357)

Full Changelog: https://github.com/gpertea/stringtie/compare/v2.2.2...v2.2.3