IsoQuant 3.3.1

Fixes UnboundLocalError: local variable 'match' referenced before assignment error in SQANTI-like output.

IsoQuant 3.3.0

• Fixed read to novel models assignment.
• Improved command line options for providing multiple files, added --prefix option.
• Additional checks for various unusual cases in input GTFs.
• Do not output empty files when no GTF is provided.

IsoQuant 3.2.0

• Unspliced novel transcripts are not reported by the default for ONT data, use --report_novel_unspliced to generate them.
• When multiple BAM/FASTQ files are provided via --bam / --fastq, they are treated as different replicas/samples of the same experiment; a single GTF and per-sample counts are generated automatically.
• 10-15 times lower RAM consumption with the same running time, thanks to @jamestwebber for refactoring and bringing attention to this!
• ~5 times lower disk consumption for temporary files.
• --low_memory option has no effect (used by default); --high_memory mimics old behavior by storing alignments in RAM.
• Read assignment reports transcript start and end (TSS/TES) matches.
• --sqanti_output generates SQANTI-like output for novel vs reference transcripts, thanks to @almiheenko!
• Resulting annotation contains exon ids.
• Supplementary gene attributes are copied from the reference annotation to the output annotations.
• Improved --resume and --force behaviour.
• --model_construction_strategy sensitive_pacbio is now more sensitive.

IsoQuant 3.1.2

• Fixed strand detection that caused lower precision for novel transcripts.
• Fixed known transcript filtering that caused lower recall for known transcripts.
• Fixed duplicate transcript entries in the output annotations.
• Fixed duplicate canonical attribute in extended annotation.
• Fix --resume option when relative paths were provided.

IsoQuant 3.1.1

• Fixed error caused by introns of length 0 (strange corner case but it does happen).
• Fixed error when using a read grouping file.
• Allow to resume a previous run from another location.

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.