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changelog.html
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<html>
<title>IsoQuant changelog</title>
<body>
<h3>IsoQuant 3.1.2, 7 February 2023</h3>
<p>Fixed strand detection that caused lower precision for novel transcripts.</p>
<p>Fixed known transcript filtering that caused lower recall.</p>
<p>Fixed duplicate transcript entries in the output annotation.</p>
<p>Fixed duplicate canonical attribute in extended annotation.</p>
<p>Fix <code>--resume</code> option when relative paths were provided.</p>
<h3>IsoQuant 3.1.1, 16 January 2023</h3>
<p>Fixed error caused by introns of length 0 (strange corner case, but it does happen).</p>
<p>Fixed error when using a read grouping file.</p>
<h3>IsoQuant 3.1.0, 3 January 2023</h3>
<p>Implement <code>--resume</code> option for resuming failed runs.</p>
<p>Fix SQANTI-like output for raw reads.</p>
<p>Fix read strand detection, improves transcript discovery as well.</p>
<h3>IsoQuant 3.0.3, 17 October 2022</h3>
<p>Simplify transcript naming, IDs of known transcripts are preserved in the output.</p>
<p>More information about novel transcripts in GTF</p>
<h3>IsoQuant 3.0.2, 10 October 2022</h3>
<p>Fix GTF attributes, thanks to @rsalz.</p>
<h3>IsoQuant 3.0.1, 31 August 2022</h3>
<p>Fix <code>--check_canonical</code> option.</p>
<h3>IsoQuant 3.0.0, 31 August 2022</h3>
<p>Annotation-free mode for de novo transcript discovery.</p>
<p>Significant speed-up.</p>
<p>Extended annotation (all reference + novel transcripts) is now part of the output.</p>
<p>Intermediate BAM files have nicer names.</p>
<p>Proper single-thread mode without thread pool usage.
<h3>IsoQuant 2.3.0, 27 May 2022</h3>
<p>New options for controlling quantification strategies. Default behaviour is changed as well. </p>
<p>New option <code>--genedb_output</code> for providing a separate folder for gene database in case the
output directory is located on a shared disk.</p>
<p>Possibility to provide read group tables in gzipped format.</p>
<h3>IsoQuant 2.2.2, 18 May 2022</h3>
<p>Fixed <code>--check_canonical</code> option.</p>
<p>Improved running time for the read assignment step (noticeable only for genes with > 100 exons).</p>
<h3>IsoQuant 2.2.1, 28 Apr 2022</h3>
<p>Minor fixes and improvement in output files. Note, that GTFs and some other files have now multiline headers.</p>
<h3>IsoQuant 2.2.0, 5 Mar 2022</h3>
<p>Parallel processing of transcript model construction phase.</p>
<p>Minor improvements in quantification of reference transcripts.</p>
<h3>IsoQuant 2.1.1, 7 Feb 2022</h3>
<p>Fixed counts/TPM for novel transcript models.</p>
<p>Fixed processing of BAM records without sequence data (e.g. secondary alignment).</p>
<p>Fixed <code>list index out of range</code> bug in long read counter.</p>
<h3>IsoQuant 2.1.0, 19 Jan 2022</h3>
<p>Improved recall by introducing relative coverage cutoffs.</p>
<p>More careful handling of transcript terminal positions.</p>
<p>Fixed GTF to BED conversion.</p>
<h3>IsoQuant 2.0.0, 7 Oct 2021</h3>
<p>Completely new transcript discovery algorithm with significantly higher recall.</p>
<p>Algorithm for read alignment correction.</p>
<p>Support for technical replicas within a single sample.</p>
<h3>IsoQuant 1.3.0, 19 Jun 2021</h3>
<p>Significantly improved running time and RAM consumption;</p>
<p>Annotation is now fed into minimap2;</p>
<p>Extended output format.</p>
<h3>IsoQuant 1.2.2, 21 May 2021</h3>
<p>Support for GFF3 mRNA features.</p>
<h3>IsoQuant 1.2.1, 21 Apr 2021</h3>
<p>Support for BAM files with =/X in CIGAR strings;</p>
<p>Fixed canonical splice site detection.</p>
<h3>IsoQuant 1.2.0, 28 Mar 2021</h3>
<p>Multi-threading;</p>
<p>Intermediate results are saved to disc to enable quick restart via --read_assignments option;</p>
<p>Significantly improved precision for novel transcript detection;</p>
<p>Secondary alignments are now used by default;</p>
<p>Fixed several bugs in inconsistency detection algorithm;</p>
<p>Reworked polyA detection and reporting once again;</p>
<p>Slightly modified read assignment output format;</p>
<p>More informative GTF output;</p>
<p>Removed --has_polya option, --polya_trimmed is now used as the opposite;</p>
<p>Added --check_canonical option.</p>
<h3>IsoQuant 1.1.0, 11 Dec 2020</h3>
<p>Significantly reworked polyA detection and reporting;</p>
<p>Improved detection of inconsistencies, added several new event types;</p>
<p>Better recall and precision for read assignment algorithm;</p>
<p>Fixed several bug and flaws;</p>
<p>Added script for counting simple stats for GTF files (srt/gtf_stats.py).</p>
<h3>IsoQuant 1.0.0, 12 Jul 2020</h3>
<p>Initial release.</p>
<p>
<a href="https://github.com/ablab/IsoQuant">IsoQuant GitHub page</a>
</p>
</body>
</html>