1

### 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