### IsoQuant 3.1.2, 7 February 2023

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.

### IsoQuant 3.1.1, 16 January 2023

Fixed error caused by introns of length 0 (strange corner case, but it does happen).

Fixed error when using a read grouping file.

### IsoQuant 3.1.0, 3 January 2023

Implement `--resume` option for resuming failed runs.

Fix SQANTI-like output for raw reads.

Fix read strand detection, improves transcript discovery as well.

### IsoQuant 3.0.3, 17 October 2022

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

More information about novel transcripts in GTF

### IsoQuant 3.0.2, 10 October 2022

Fix GTF attributes, thanks to @rsalz.

### IsoQuant 3.0.1, 31 August 2022

Fix `--check_canonical` option.

### IsoQuant 3.0.0, 31 August 2022

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.

### IsoQuant 2.3.0, 27 May 2022

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.

### IsoQuant 2.2.2, 18 May 2022

Fixed `--check_canonical` option.

Improved running time for the read assignment step (noticeable only for genes with > 100 exons).

### IsoQuant 2.2.1, 28 Apr 2022

Minor fixes and improvement in output files. Note, that GTFs and some other files have now multiline headers.

### IsoQuant 2.2.0, 5 Mar 2022

Parallel processing of transcript model construction phase.

Minor improvements in quantification of reference transcripts.

### IsoQuant 2.1.1, 7 Feb 2022

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.

### IsoQuant 2.1.0, 19 Jan 2022

Improved recall by introducing relative coverage cutoffs.

More careful handling of transcript terminal positions.

Fixed GTF to BED conversion.

### IsoQuant 2.0.0, 7 Oct 2021

Completely new transcript discovery algorithm with significantly higher recall.

Algorithm for read alignment correction.

Support for technical replicas within a single sample.

### IsoQuant 1.3.0, 19 Jun 2021

Significantly improved running time and RAM consumption;

Annotation is now fed into minimap2;

Extended output format.

### IsoQuant 1.2.2, 21 May 2021

Support for GFF3 mRNA features.

### IsoQuant 1.2.1, 21 Apr 2021

Support for BAM files with =/X in CIGAR strings;

Fixed canonical splice site detection.

### IsoQuant 1.2.0, 28 Mar 2021

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.

### IsoQuant 1.1.0, 11 Dec 2020

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).

### IsoQuant 1.0.0, 12 Jul 2020

Initial release.

IsoQuant GitHub page