FLAIR Release 3.0.0

[diekhans]

[v3.0.0] 2025-11-31

• General
  • Bug fixes since v3.0.0b1
  • Removed dependencies on pandas and rpy2.
  • Added proper logging throughout
• FLAIR align
  • Cleaned up output files - now outputs unfiltered BAM and filtered BED
• FLAIR correct
  • Changed orthogonal junction inputs - now specify whether your file is
    a bed (--junction_bed) or whether it comes from STAR short-read RNA alignment (--junction_tab)
  • Now support detecting junctions directly from long read data:
    run intronProspector to generate junction bed, input that via --junction_bed,
    specify desired junction read support with --junction_support
  • Removed -g genome option, increases speed
  • Now produces sorted output files
• FLAIR collapse
  • cleaned up output files, now only gives: isoforms.bed, isoforms.gtf, isoforms.fa, isoform.read.map.txt
  • (experimental) added filter for removing reads with internal priming.
    Options: --remove_internal_priming, --intprimingthreshold, --intprimingfracAs
  • allow CDS prediction in collapse with --predictCDS
  • removed genomic range option (too fragile). For parallelization, run FLAIR transcriptome
  • made gtf (annotation) parsing more robust, especially for unsorted files
  • improved fractional support filtering (with --support < 1)
  • improved isoform haplotyping through longshot - this is being deprecated though, please use FLAIR variants
• FLAIR quantify
  • improved fraction of reads assigned to isoforms and recovered (better handling of ambiguous alignments)
  • improved processing of multiple samples so running requires less available memory and is faster
• FLAIR diffexp and diffsplice
  • recoded directly in R to improve performance
• New modules
  • FLAIR transcriptome
    • Combines the functions of correct and collapse
    • Runs directly from an aligned BAM file
    • Performs more effective parallelization (specify in --parallelmode)
  • FLAIR fusion
    • Detects gene fusions and fusion isoforms
    • Fusion detection accuracy is comparable to JAFFAL and CTAT-lr-fusion
    • Fusion isoform detection is much more accurate
  • FLAIR combine
    • Allows combining transcriptomes generated from different samples
    • Fusion isoforms can be combined with collapsed isoforms to form a full transcriptome
    • Manipulate filtering of single exon isoforms with --include_se
  • FLAIR variants
    • Allows detection of variant-aware transcripts through
      identification of read clusters with shared variants
    • Uses variants detected either from WGS or from lr-RNA-seq.
      We recommend Longshot.
    • Good for identifying splicing of specific variants
    • Can be used in conjunction with FLAIR diffexp or diff_iso_usage
      to identify changes in variant-aware transcripts between samples/groups
• Added FLAIR protocol to improve guidance on running flair

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This discussion was created from the release FLAIR Release 3.0.0.