changelog.md

IsoQuant changelog

IsoQuant 3.4.1, 9 May 2024

• Fixes IndexError: list index out of range when --sqanti_output is set (#186).

• Fixes IndexError: list index out of range in printing grouped transcript models TPMs (#187).

• Reduced running time when --sqanti_output is set.

IsoQuant 3.4.0, 9 May 2024

Major novelties and improvements:

• Significant speed-up on datasets containing regions with extremely high coverage, often encountered on mitochondrial chromosomes (#97).

• Added support for Illumina reads for spliced alignment correction (thanks to @rkpfeil).

• Added support YAML files (thanks to @rkpfeil). Old options --bam_list and --fastq_list are still availble, but deprecated since this version.

Transcript discovery and GTF processing:

• Fixed missing genes in extended GTF (#140, #147, #151, #175).

• Fixed strand detection and output of transcripts with . strand (#107).

• Added --report_canonical and --polya_requirement options that allows to control level of filtering of output transcripts based on canonical splice sites and the presence of poly-A tails. (#128)

• Added check for input GTFs (#155).

• Extract CDS, other features and attributes from reference GTF to the output GTFs (#176).

• Reworked novel gene merging procedure (#164).

• Revamped algorithm for assigning reads to novel transcripts and their quantification (#127).

Read assignment and quantification:

• Optimized read-to-isoform assignment algorithm.

• Added gene_assignment_type attribute to read assignments.

• Fixed duplicated records in read_assignments.tsv (#168).

• Improved gene and transcript quantification. Only unique assignments are now used for transcript quantification. Added more options for quantification strategies (--gene_quantification and --transcript_quantification).

• Improved consistency between trascript_counts.tsv and transcript_model_counts.tsv (#137).

• Introduced mapping quality filtering: --min_mapq, --inconsistent_mapq_cutoff and --simple_alignments_mapq_cutoff (#110).

Minor fixes and improvements:

• Added --bam_tags option to import additional information from BAM files to read assignments output.

• Large output files are now gzipped by default, --no_gzip can be used to keep uncompressed output (#154).

• BAM stats are now printed to the log (#139).

• Various minor fixes and requests (#106, #141, #143, #146, #179).

Special acknowledgement to @almiheenko for testing and reviewing PRs, and to @alexandrutomescu for supporting the project.

IsoQuant 3.3.1, 26 July 2023

• Fixed UnboundLocalError: local variable 'match' referenced before assignment error in SQANTI-like output.

IsoQuant 3.3, 13 June 2023

• Fixed read to novel models assignment.

• Improved command line options for providing multiple files, added --prefix option.

• Additional checks for various unusual cases in input GTFs.

• Do not output empty files when no GTF is provided.

IsoQuant 3.2, 27 March 2023

• Unspliced novel transcripts are not reported by the default for ONT data, use --report_novel_unspliced to generate them.

• When multiple BAM/FASTQ files are provided via --bam / --fastq, they are treated as different replicas/samples of the same experiment; a single GTF and per-sample counts are generated automatically.

• 10-15 times lower RAM consumption with the same running time.

• ~5 times lower disk consumption for temporary files.

• --low_memory option has no effect (used by default); --high_memory mimics old behavior by storing alignments in RAM.

• Read assignment reports transcript start and end (TSS/TES) matches.

• --sqanti_output generates SQANTI-like output for novel vs reference transcripts.

• Resulting annotation contains exon ids.

• Supplementary gene attributes are copied from the reference annotation to the output annotations.

• Improved --resume and --force behaviour.

• --model_construction_strategy sensitive_pacbio is now more sensitive.

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