CTAT-LR-Fusion v1.4.0

• updates to yield more deterministic behavior around tie-breaking and output ordering.

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

CTAT-LR-Fusion v1.3.0

CTAT-LR-fusion v1.3.0 Feb 3, 2026

• more rigorous filtering of foldback-type alignments
• added --max_rigor to force using all reads and whole genome decoy in 2nd phase
• can incorporate target fusions or only focus on specific fusions via --incl_fusion_targets or --only_fusion_targets

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

CTAT-LR-Fusion v1.2.1

CTAT-LR-fusion v1.2.1 Setp 15, 2025

• when min FFPM set to zero, limits to 10k candidates
• uses FusionInspector contig builder that's much faster using a preloaded genome instead of per-contig region retrievals
• overhaul to leverage max number of phase 1 candidates and perform read-based and annot-based filtering before applying the max candidate cutoff
• adding --frac_FFPM_phase1 for soft phase 1 thresholding
• uses gzipped fasta and fastqs to save disk space

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

CTAT-LR-Fusion v1.1.2

CTAT-LR-Fusion v1.1.2 Aug 7, 2025

• respect the --min_num_LR and --min_LR_novel_junction_support and ensure --min_LR_novel_junction_support always >= --min_num_LR

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

CTAT-LR-Fusion release v1.1.1

• minor update to ctat-minimap2 to resolve compilation error.

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

ctat-LR-fusion v1.1.0 release

CTAT-LR-Fusion v1.1.0 Feb 10, 2025

• allow --LR_bam for providing a pre-aligned minimap2 bam file to kickstart a run and skip most of the initial ctat-LR-fusion phase-1 computes. (Thanks Sergey Aganezov again!)

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

ctat-LR-fusion v1.0.2 Release

• use less RAM by:
  • dont load entire alignment gff3 file into ram at once, instead process one alignment target at a time
  • update to ctat-mm2 to fix memory leak
    (Thanks Sergey Aganezov for reporting and testing issues!)

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

ctat-LR-fusion-v1.0.1

ctat-LR-fusion v1.0.1 Dec 31, 2024

• bugfix wrt igv-prep and igv html for vis of long reads
• sync'd latest minimap2 to ctat-minimap2

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

CTAT-LR-Fusion Release v1.0.0

ctat-LR-fusion v1.0.0 Oct 8, 2024

• works well for both ONT and PacBio under default params.
• excludes alignment overlaps between gene pairs that fall within sequence-similar regions, and requires at least 25 bases (default) of exon overlap in the remaining regions.
• excluding neighbor-overlap gene pairings and additional annotation-based filtering between phase-1 and phase-2.
• added --FI_extra_params custom parameter to pass through STAR parameters to F
• included option for --examine_coding_effect

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules

CTAT-LR-Fusion v0.13.0

ctat-LR-fusion v0.13.0 Jan 27, 2024

• allow for paralog alignments to be included
• pursue additional candidates where one breakpoint is initially <= MAX_EXON_DELTA and the other is within 1kb and there's multiple reads suggesting it.
• with multiple reads suggesting fusion, use the min value for the deltas in phase 1 for candidate selection.
• reorganization of preliminary candidate intermediate output formatting for easier tracking and troubleshooting of findings.
• igv-reports v1.11.0 which has default ordering of fusions according to descending read support in the html.

Preferred ctat genome lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v22_CTAT_lib_Mar012021.STAR_v2.7.11a.plug-n-play.tar.gz

** Download the FULL version ** as it contains all required submodules