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Tools used in IsoTV

IsoTV incorporates many external tools. Below are descriptions and references to all the tools that were used.

ONT Reads Processing

  • Filtlong - Filtering reads by their quality.
  • Pychopper - Finding full length transcripts.
  • Pinfish - Obtaining transcription using genome-based transcript polishing.
  • Gffcompare - Comparing obtained transcription to existing annotation.
  • Minimap2 - Mapping reads to a de novo defined transcriptome.
  • DeSeq2 - Normalize isoform expression across samples.

Functional Feature Analysis

  • ScanProsite - Identify potential protein functional sites and motifs from the PROSITE database.
  • InterProScan - Command line version of InterPro, allowing to predict protein function using data gathered from many different resources. Used for Pfam protein domain prediction.
  • Brewery - Protein secondary structure prediction.
  • IUPred2A - Identify regions of disorder.