IsoQuant 1.2

• 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

• 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

Initial release of IsoQuant.