IsoQuant 3.4.1

Instant bug-fix release for 3.4.0

• 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.

All new major features of 3.4.0

IsoQuant 3.4.0

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).

• New option to control TPM computing (--normalization_method).

• 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

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

IsoQuant 3.3.0

• 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 3.2.0

• 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, thanks to @jamestwebber for refactoring and bringing attention to this!
• ~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, thanks to @almiheenko!
• 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

• Fixed strand detection that caused lower precision for novel transcripts.
• Fixed known transcript filtering that caused lower recall for known transcripts.
• Fixed duplicate transcript entries in the output annotations.
• Fixed duplicate canonical attribute in extended annotation.
• Fix --resume option when relative paths were provided.

IsoQuant 3.1.1

• Fixed error caused by introns of length 0 (strange corner case but it does happen).
• Fixed error when using a read grouping file.
• Allow to resume a previous run from another location.

IsoQuant 3.1.0

• Implemented --resume option for resuming failed runs.
• Fixed SQANTI-like output for raw reads.
• Fixed read strand detection, improves transcript discovery as well.

IsoQuant 3.0.3

• Simplify transcript naming, IDs of known transcripts are preserved in the output.

• More information about novel transcripts in GTF, i.e. similar reference transcripts and splicing modification types.

IsoQuant 3.0.2

Bug-fix release:

• Fixes GTF attributes, thanks to @rsalz.