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

CTAT-LR-fusion v0.12.0

ctat-LR-fusion v0.12.0, Jan 2, 2024

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

Release notes:

• igv html working with long and short reads together
• results sorted by descending countws of supporting reads
• in combined long/short mode, retain any fusion calls with illumina reads that meet the min read requirements regardless of dominant isoform fraction results
• added option --chim_candidates_only to just get the initial list of chimeric candidate

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

ctat-LR-fusion Release v0.11.0

ctat-LR-fusion v0.11.0 Oct 12, 2023

• leaner on disk space usage by sam->bam streamed
• include igv files bundle as output
• adding LeftGene and RightGene info thats retained on short read integration
• allow secondary alignments in phase 2 (important for retaining read support abundance across paralogs)

Compatible with ctat genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

which uses STAR v2.7.8a as per: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

and be sure to update your AnnotFilterRule.pm in the ctat genome lib as per: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/00__README.txt

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

ctat-LR-fusion Release v0.10.0

ctat-LR-fusion v0.10.0 Aug 19, 2023

• more optimization of ctat-minimap2
• bugfix to ROI definition off-by-one on acceptor site for igv-report display
• include LeftGene and RightGene columns
• added get_MAS-seq_fusion_cell_barcoding.py for supporting sc-MAS-seq analysis (single cells and long reads)

Compatible with ctat genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

which uses STAR v2.7.8a as per: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

and be sure to update your AnnotFilterRule.pm in the ctat genome lib as per: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/00__README.txt

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

ctat-LR-fusion Release v0.9.0

ctat-LR-fusion Release v0.9.0

• ctat-minimap2 performance enhancements
• includes default filtering at the 0.1 FFPM threshold
• igv-reports upgrade, better performance and highlight fusion breakpoints as ROIs

Compatible with ctat genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

which uses STAR v2.7.8a as per: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

and be sure to update your AnnotFilterRule.pm in the ctat genome lib as per: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/00__README.txt

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

ctat-LR-fusion Release v0.6.0

ctat-LR-fusion v0.6.0

• bugfixes for non-ref-splice coordinate assignments
• added option: --snap_dist : if breakpoint is at most this distance from a reference exon boundary, position gets snapped to the splice site.
• added option: --min_frac_dom_iso_expr : minimum expression of dominant isoform (default: 0.05)
• adjusted minimap2 alignment params used.
• exits gracefully if no fusions found in initial phase.
• cleaner organization of IGV-prep files.

Compatible with ctat genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

which uses STAR v2.7.8a as per: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

and be sure to update your AnnotFilterRule.pm in the ctat genome lib as per: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/00__README.txt

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