GAP-MS

GAP-MS uses mass-spectrometry peptides to assess gene predictions, combine annotations and identify peptide-supported changes for review.

Install

Python 3.10 or newer:

pip install gapms==1.3.2

For runs with a BAM file, also install the RNA reconstruction tools:

conda install -c conda-forge -c bioconda stringtie transdecoder=5.5.0

Alternatively, build an Apptainer image from this checkout. It includes these tools:

apptainer build --fakeroot gapms-1.3.2.sif gapms.def
apptainer run gapms-1.3.2.sif -a assembly.fa -p peptides.tsv -g genes.gtf

Version 1.3.2 must be uploaded to PyPI before the pip command above is available. See container instructions for Docker Hub.

Run

• Assembly + peptides: map peptides to the six-frame genome translation. gapms -a assembly.fa -p peptides.tsv
• Add BAM: include RNA-supported splice paths and reconstruct peptide-supported ORF candidates. gapms -a assembly.fa -p peptides.tsv -b sorted.bam
• Add annotation: map across annotated exons, score gene models and propose supported changes. gapms -a assembly.fa -p peptides.tsv -g genes.gtf
• Annotation + BAM: combine gene-model assessment with RNA-supported reconstruction. gapms -a assembly.fa -p peptides.tsv -g genes.gtf -b sorted.bam
• Multiple annotations: automatically build a peptide-guided consensus. BAM is optional here too. gapms -a assembly.fa -p peptides.tsv -g helixer.gtf -g another.gff3

GTF and GFF3 are accepted. BAM files must be coordinate-sorted and use the assembly's sequence names. FragPipe, Casanovo and plain peptide lists are supported. Use -o results to choose an output directory (default: ./GAPMS_output) and -t 16 to change the default of 8 threads.

Analysis uses trypsin-compatible exact matches by default; add --non-tryptic for other enzymes. Isoleucine and leucine are treated as equivalent. All-match and tryptic-match BED tracks are always retained. Optional one-edit rescue is separate from the exact evidence used to support gene models. See gapms --help-all.

Results

Start with report.html; report.log records the run. Main outputs include peptides.bed, peptides.tryptic.bed, peptides.igv.bed, unmapped_peptides.tsv, and, when gene models are available, all_proteins_scores.tsv and supported_genes.gtf. Multiple annotations also produce consensus.gff3 and consensus_proteins.faa.

review/ contains supported novel/alternative proposals when available. They require review and are not automatically applied. Existing annotated isoforms are considered before proposing changes. Without an input annotation, RNA-derived ORFs are candidates whose novelty cannot be assessed. Peptide support does not validate every boundary of a gene model.

Technical guide · Five-mode validation of 1.3.2

Cite

GAP-MS manuscript on bioRxiv