IsoQuant 3.1.0

• Implemented --resume option for resuming failed runs.
• Fixed SQANTI-like output for raw reads.
• Fixed read strand detection, improves transcript discovery as well.

IsoQuant 3.0.3

• Simplify transcript naming, IDs of known transcripts are preserved in the output.

• More information about novel transcripts in GTF, i.e. similar reference transcripts and splicing modification types.

IsoQuant 3.0.2

Bug-fix release:

• Fixes GTF attributes, thanks to @rsalz.

IsoQuant 3.0.1

Bug-fix release. Fixes --check_canonical option.

IsoQuant 3.0

• Annotation-free mode is implemented.
• Lower RAM consumption and better running time.
• Proper single-thread mode.

IsoQuant 2.3.0

• New options for controlling quantification strategies. Default behavior is changed as well.
• New option --genedb_output for providing a separate folder for gene database in case the output directory is located on a shared disk.
• Possibility to provide read group tables in gzipped format.

IsoQuant 2.2.2

A bug-fix release:

• Fixed --check_canonical option.
• Improved running time for the read assignment step (noticeable only for genes with > 100 exons).

IsoQuant 2.2.1

Bug-fix release. No meaningful changes since 2.2.0.
Contains minor fixes and improvement in output files. Note, that GTFs and some other files have now multiline headers.

IsoQuant 2.2

• Parallel processing of transcript model construction phase.
• Minor improvements in quantification of reference transcripts.

IsoQuant 2.1.1

• Fixed counts/TPM for novel transcripts.
• Fixed processing BAM records without sequence data (e.g. secondary alignments).
• Fixed list index out of range bug in long read counter.