IsoQuant Files

Major novelties and improvements:

• Significant speed-up on datasets containing regions with extremely high coverage,often encountered on mitochondrial chromosomes (https://github.com/ablab/IsoQuant/issues/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 (https://github.com/ablab/IsoQuant/issues/140, https://github.com/ablab/IsoQuant/issues/147, https://github.com/ablab/IsoQuant/issues/151, https://github.com/ablab/IsoQuant/issues/175).

• Fixed strand detection and output of transcripts with . strand (https://github.com/ablab/IsoQuant/issues/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. (https://github.com/ablab/IsoQuant/issues/128).

• Added check for input GTFs (https://github.com/ablab/IsoQuant/issues/155).

• Extract CDS, other features and attributes from reference GTF to the output GTFs (https://github.com/ablab/IsoQuant/issues/176).

• Reworked novel gene merging procedure (https://github.com/ablab/IsoQuant/issues/164).

• Revamped algorithm for assigning reads to novel transcripts and their quantification (https://github.com/ablab/IsoQuant/issues/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 (https://github.com/ablab/IsoQuant/issues/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 (https://github.com/ablab/IsoQuant/issues/137).

• Introduced mapping quality filtering: --min_mapq, --inconsistent_mapq_cutoff and --simple_alignments_mapq_cutoff (https://github.com/ablab/IsoQuant/issues/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 (https://github.com/ablab/IsoQuant/issues/154).

• BAM stats are now printed to the log (https://github.com/ablab/IsoQuant/issues/139).

• Various minor fixes and requests: https://github.com/ablab/IsoQuant/issues/106, https://github.com/ablab/IsoQuant/issues/141, https://github.com/ablab/IsoQuant/issues/143, https://github.com/ablab/IsoQuant/issues/146, https://github.com/ablab/IsoQuant/issues/179.

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