IsoQuant 3.6.2

Important bug-fix release!

Fixes linear grouped counts output #258, big thanks to @qsonehara!

IsoQuant 3.6.1

• Import exon attributes from the reference annotation #175

• Fixed annotation checks for GFF3 #240

IsoQuant 3.6.0

Fixes #236 by resolving duplicated noninformative and intergenic reads assignments.
As a results, also fixes duplicated novel transcripts. Thanks @jamestwebber for the report!

IsoQuant 3.5.2

Fixes exon counting algorithm #229, thanks to @skagawa2!

IsoQuant 3.5.1

• Fix YAML support in visualization #222

• Fix transcript naming when IsoQuant-generated GTF is provided as input #219

• Fix exons attribute duplication #219

• Exon ids are now consistent between output and input annotations if present

• New --count_format option for setting desired grouped counts format (matrix/linear/both), fixes #223

IsoQuant 3.5.0

• New visualization software developed by @jackfreeman88. See more here.

• Dramatically reduced RAM consumption for grouped counts, about 10-20x decrease on datasets with large number of groups.
  Important fix for single-cell data processing. Should fix #189.

• Fixed #195: output GTF contained very similar isoforms and estimated their expression as 0.

• New documentation is now available at ablab.github.io/IsoQuant.

IsoQuant 3.4.2

• Dramatically reduce RAM consumption. Should fix #209.

  IsoQuant 3.4.2 was tested on a simulated ONT dataset with 30M reads using 12 threads. In the default mode RAM consumption decreased from 280GB to 12GB when using the reference annotation and from 230GB down to 6GB in the reference-free mode. Running time in the default mode increased by approximately 20-25%. When using --high_memory option, running time remains the same as in 3.4.1, RAM consumption in the reference-based mode is 46GB, and 36GB in the reference-free mode. Note, that in general RAM consumption depends on the particular data being used and the number of threads.

  In brief, in 3.4.0 and 3.4.1 inadequate RAM consumption was caused by this commit. Apparently, adding a couple of int fields to the BasicReadAssignment class made the default pickle serialization not to clean used memory (possibly, a leak). Since some large lists of BasicReadAssignment were sent between processes, this caused the main process to consume unnecessary RAM. When later new processes were created for GTF construction, total RAM consumption exploded thanks to the way Python multiprocessing works. This release implements two ways fixing the issue: sending objects via disk (default) and using custom pickle serialization (when --high_memory is used).

• Transcript and exon ids are now identical between runs, including ones with different number of threads.

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.