AsaruSim v1.0

New

• Simulate the intron retention process
• Simulate unspliced transcripts
• Handle novel isoform count matrix if an assembled GTF file is provided
• Model transcript truncation

Update

• Replaced the GTF parser function with the HTSeq reader module for improved flexibility
• Aligned reads to the transcriptome instead of the genome to model errors
• Enabled gzip compression for output files

Add

• Unit tests for principal functions
• Pipeline trace, timeline and Dag

Fix

• Resolved the PCR total reads issue
• Ensured the length_dis option is passed to the fetch_transcript_id_by_gene function

AsaruSim v0.2.1

Fixes

• Corrected the AsaruSim version.
• Passed the correct on_disk option to transcriptome_init.
• Updated figure axis names in the QC HTML report.

Additions

• Added a script to run with the paper dataset.

AsaruSim v0.2.0

• Added functionality to handle SPARSim preset matrices.
• Added a helper function for the Nextflow workflow.
• Fixed a bug where GTF entries without a gene_name caused errors.
• Introduced a new report design for improved traceability.

Asaru v0.1

• Initial release:
  • Nextflow workflow
  • ADD: BC,UMI, features ground truth
  • ADD: Full length read distribution
  • QC report

Full Changelog: v1.0...v1.0