Download Latest Version IsoQuant 3.12.2 source code.tar.gz (6.4 MB)
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IsoQuant-3.2.0.tar.gz 2023-03-29 1.0 MB
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IsoQuant 3.2.0 source code.tar.gz 2023-03-29 1.1 MB
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IsoQuant 3.2.0 source code.zip 2023-03-29 1.1 MB
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README.md 2023-03-29 1.1 kB
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Totals: 4 Items   3.2 MB 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.
Source: README.md, updated 2023-03-29