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.
~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.
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.
Fixed strand detection that caused lower precision for novel transcripts.
Fixed known transcript filtering that caused lower recall.
Fixed duplicate transcript entries in the output annotation.
Fixed duplicate canonical attribute in extended annotation.
Fix --resume option when relative paths were provided.
Fixed error caused by introns of length 0 (strange corner case, but it does happen).
Fixed error when using a read grouping file.
Implement --resume option for resuming failed runs.
Fix SQANTI-like output for raw reads.
Fix read strand detection, improves transcript discovery as well.
Simplify transcript naming, IDs of known transcripts are preserved in the output.
More information about novel transcripts in GTF
Fix GTF attributes, thanks to @rsalz.
Fix --check_canonical option.
Annotation-free mode for de novo transcript discovery.
Significant speed-up.
Extended annotation (all reference + novel transcripts) is now part of the output.
Intermediate BAM files have nicer names.
Proper single-thread mode without thread pool usage.
New options for controlling quantification strategies. Default behaviour 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.
Fixed --check_canonical option.
Improved running time for the read assignment step (noticeable only for genes with > 100 exons).
Minor fixes and improvement in output files. Note, that GTFs and some other files have now multiline headers.
Parallel processing of transcript model construction phase.
Minor improvements in quantification of reference transcripts.
Fixed counts/TPM for novel transcript models.
Fixed processing of BAM records without sequence data (e.g. secondary alignment).
Fixed list index out of range bug in long read counter.
Improved recall by introducing relative coverage cutoffs.
More careful handling of transcript terminal positions.
Fixed GTF to BED conversion.
Completely new transcript discovery algorithm with significantly higher recall.
Algorithm for read alignment correction.
Support for technical replicas within a single sample.
Significantly improved running time and RAM consumption;
Annotation is now fed into minimap2;
Extended output format.
Support for GFF3 mRNA features.
Support for BAM files with =/X in CIGAR strings;
Fixed canonical splice site detection.
Multi-threading;
Intermediate results are saved to disc to enable quick restart via --read_assignments option;
Significantly improved precision for novel transcript detection;
Secondary alignments are now used by default;
Fixed several bugs in inconsistency detection algorithm;
Reworked polyA detection and reporting once again;
Slightly modified read assignment output format;
More informative GTF output;
Removed --has_polya option, --polya_trimmed is now used as the opposite;
Added --check_canonical option.
Significantly reworked polyA detection and reporting;
Improved detection of inconsistencies, added several new event types;
Better recall and precision for read assignment algorithm;
Fixed several bug and flaws;
Added script for counting simple stats for GTF files (srt/gtf_stats.py).
Initial release.