Arriba v2.4.0

• new utility script to annotate exon numbers
• compatibility with Illumina's Dragen aligner (see notes in manual about supported aligners)
• retained fraction of protein domain was often overestimated as 100%
• better agreement of transcripts between Arriba's output file and the visualizations produced by draw_fusions.R by making --transcriptSelection=provided the default
• better matching of structural variant breakpoints to fusion breakpoints when parameter -d is used
• VCF files generated by scripts/convert_fusions_to_vcf.sh are now compatible with bcftools
• mildly improved filtering

Arriba v2.3.0

• blacklist PhiX genome, since it is often used as spike-in control
• stricter filtering of read-through fusions
• fix broken compilation due to outdated zlib URL (thanks to @iainrb)
• updated protein domain annotation files (GFF3), now with 7-15% more annotation records
• updated reference files in download_references.sh to match protein domain annotation version
• download_references.sh did not properly harmonize chromosome names between assembly (FastA) and annotation (GTF) when an assembly with chr prefix was used (hg19/38, mm10/39), which had minor implications on alignment and fusion calling
• coverage plots can be scaled separately and/or to a user-defined cutoff (--coverageRange=...)
• scripts are now compatible with macOS (a recent version of bash must be installed, though; the preinstalled version 3.2 is too old)
• minor fixes for reading frame prediction when breakpoint is close to first/last exon

Arriba v2.2.1

• reverted a change introduced in v2.2.0: download_references.sh now uses the ENSEMBL GRCh38 assembly (FastA) again instead of the ICGC-ARGO assembly, because the latter contains ALT contigs, which is not recommended for alignment using STAR according to the STAR user manual; moreover, due to scripting error, the GRCh38 assembly generated by downloaded_references.sh contained malformed data at the end of the file, which is now fixed as well

Arriba v2.2.0

• improved detection of internal tandem duplications
• better sensitivity for the detection of viral integration sites
• inclusion of additional ~4500 viruses into screening, including rare strains of cancer-associated viruses (requires rebuild of STAR index)
• viral contigs were renamed to be compliant with the SAM format specification (requires rebuild of STAR index)
• support for mm39/GRCm39
• utility scripts (see also manual):
  • quantify virus expression
  • convert Arriba's custom output format to VCF
  • extract fusion-supporting alignments into separate mini-BAM
  • running Arriba on a prealigned BAM file and realigning only the fusion candidate reads saves ~80% of the CPU time compared to a complete realignment (useful when the alignments were generated by an old STAR version or by a different aligner such as HISAT2)
• polishing of fusion visualizations created by draw_fusions.R and new features:
  • all transcripts can be drawn at the same scale if desired (--fixedScale)
  • circos plots have same size across all pages
  • set PDF title and print as header on every page (--sampleName)
  • fine-grained control over region to draw for intergenic breakpoints (--showIntergenicVicinity)
  • choose a different font (--fontFamily)
  • better scaling for coverage track
• more fixes for prediction of reading frame
• better warnings and error messages
• updated STAR to version 2.7.10a, which fixes malformed chimeric alignments for paired-end reads with small insert size
• updated dependencies (HTSlib, libdeflate)

Arriba v2.1.0

• Arriba can now be cited
• arcs in circos plot are colored by type of rearrangement
• internal tandem duplications are flagged with the keyword ITD in Arriba's output file
• more effective filtering of germline polymorphism internal tandem duplications
• draw_fusions.R loads reference files faster
• under some rare conditions, the reading frame was erroneously predicted as out-of-frame

Arriba v2.0.0

• report viral integration sites
• report fusions supported by multi-mapping reads (e.g., CIC-DUX4, NPM1-ALK)
• report internal tandem duplications (e.g., FLT3, BCOR, ERBB2, NOTCH1)
• improved detection of IG/TCR rearrangements
• known fusions file based on the Mitelman database is now part of the download
• more comprehensive annotation (gene IDs, transcript IDs, user-defined tags, retained protein domains)
• support for mouse (mm10)
• (optionally) report the full transcript/peptide sequence (parameter -I) rather than only what can be assembled from the supporting reads
• structural variants can be supplied in VCF format (parameter -d)
• MacOS support
• faster loading of BAM files thanks to HAT-trie map as well as other speed improvements
• draw_fusions.R accepts the format of STAR-Fusion
• ability to make use of external duplicate marking, e.g., for UMIs (parameter -u)
• enhanced blacklist
• simplified code compilation procedure
• support assemblies with up to 65,000 contigs (previously 32,000)

Important compatibility notes when upgrading from version 1.x:

• STAR version >= 2.7.6a is required to make use of multi-mapping chimeric reads
• new columns were added to the output files and some were rearranged
• the parameter -P is obsolete; the parameters -I and -T have been repurposed
• parsing of input TSV files (GTF, known fusions, blacklist, structural variants) is now stricter
• the order of the genes in the known fusions file (parameter -k) is now important
• the reading_frame column may contain the new value stop-codon
• the site1/2 columns may contain new values
• the parameters of the run_arriba.sh script have changed
• the download_references.sh script is now parameterized using environment variables
• the chr prefix is no longer removed from the output files
• the alignment parameters of run_arriba.sh are set to report up to 50 multi-mapping reads
• some filters were removed/renamed, which is relevant if the parameter -f is used

Arriba v1.2.0

• better filtering of in vitro-generated artifacts
• known_fusions filter is more sensitive
• update dependencies (HTSlib, compression libs)
• example data
• under some (rare) conditions, reading frame was incorrect
• documentation provides tips on how to interpret fusion predictions
• better error messages for common cases of incorrect usage

Arriba v1.1.0

• speed improvements (BAM file loading, low_entropy filter, homologs filter, GTF parsing)
• prebuilt Docker image available at Docker Hub
• installation via bioconda
• improved confidence scoring
• better detection of intragenic rearrangements
• new blacklist
• fix some non-deterministic behavior
• more reliable auto-detection of strandedness
• protein domains were drawn in incorrect order for genes on the reverse strand
• handle empty input files more reasonably

Arriba v1.0.1

• fix bugs in parsing of command-line arguments
• do not compress intermediate (unsorted) BAM file to avoid performance bottleneck

Arriba v1.0.0

• streamlined workflow (extract_read-through_fusions is obsolete)
• generate publication-quality figures of fusions
• predict peptide sequences
• protein domain track for loading into IGV
• Singularity recipe
• CRAM support
• simplified installation procedure
• fix off-by-one error (=> new blacklists!)
• improved sensitivity/specificity