IsoQuant 2.3.0

• New options for controlling quantification strategies. Default behavior 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

A bug-fix release:

• Fixed --check_canonical option.
• Improved running time for the read assignment step (noticeable only for genes with > 100 exons).

IsoQuant 2.2.1

Bug-fix release. No meaningful changes since 2.2.0.
Contains minor fixes and improvement in output files. Note, that GTFs and some other files have now multiline headers.

IsoQuant 2.2

• Parallel processing of transcript model construction phase.
• Minor improvements in quantification of reference transcripts.

IsoQuant 2.1.1

• Fixed counts/TPM for novel transcripts.
• Fixed processing BAM records without sequence data (e.g. secondary alignments).
• Fixed list index out of range bug in long read counter.

IsoQuant 2.1

• Improved recall by introducing relative coverage cutoffs.
• More careful handling of transcript terminal positions.
• Fixed GTF to BED conversion.

IsoQuant 2.0

This is significantly upgraded version of IsoQuant, which includes:

• completely new transcript discovery algorithm with significantly higher recall and precision;
• algorithm for read alignment correction;
• support for technical replicas within a single sample.

IsoQuant 1.3

-Significantly improved running time and RAM consumption;
-Annotation is now fed into minimap2;
-Extended output format.

IsoQuant 1.2.2

A bug-fix release for GFF3 format.

IsoQuant 1.2.1

Bug-fix release:

• Support for BAM files with =/X in CIGAR strings;
• Fixed canonical splice site detection.