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Version 1.7.2 – bugfix 5
Bug Fixes:
• Fixed an error in personalized proteome generation (AnnotateDinucleotideVariants) caused by misannotated transcripts (in GENCODE).
• Fixed incorrect parsing of some germline variants in AnnotateFragPipePeptides, which could lead to failures.
• Fixed handling of phased variants leading to premature stop codons in AnnotateFragPipePeptides, which previously caused inconsistent outputs and errors.
• Fixed a bug when merging MS-identified peptides across multiple samples when peptides mapped to genes from different organisms.
Improvements:
• Improved error handling when too few variants are detected: the pipeline now reports a clear message; If MS analysis is enabled, the pipeline now proceeds with immunopeptidomics analysis even when variant counts are insufficient, then stops gracefully (no report or Excel prioritization file generated).
Version 1.7.2 – bugfix 4
Bug Fixes:
• Fixed an error in the merging of immunopeptidomics data
• Clarified long peptides ranking by only ranking optimal long peptide sequences (and not ranking additional long peptide sequences)
Version 1.7.2 – bugfix 3
Bug Fixes:
• Improved immunopeptidomics summary and plots, reporting number of identifications per injection type, instead of based on predictions (i.e. HLA-II predicted peptides identified in HLA-I injections are not reported in the QC)
• Fixed an error in the analysis of TIMSTOF DIA data
• Fixed an error where MSidentified cancer-specific-pc peptides were not reported in the table, after merging samples analysis
• Fixed a rare error in the plotting of HLA-LOH (personalized proteome)
Version 1.7.2 – bugfix 2
Bug Fixes:
• Fixed a rare error where an HLA-typed allele appears as non-available
Version 1.7.2 – bugfix 1
Bug Fixes:
• Fixed an error in the parsing of the configuration file during the MS statistics part
• Improved reliability of the copy of MS data
Version 1.7.2
Version 1.7.2 introduces support for Bruker timsTOF data analysis and adresses bugs identifier in earlier versions.
Major changes:
• Support for Bruker timsTOF data:
• Bruker timsTOF data are specified in the following variable in the configuration file: MS_SPECTRA_TIMSTOF_DDA_HLA_I, MS_SPECTRA_TIMSTOF_DDA_HLA_II, MS_SPECTRA_TIMSTOF_DIA_HLA_I, MS_SPECTRA_TIMSTOF_DIA_HLA_II
• Thermo Orbitrap data keep the same variable names in the configuration file: MS_SPECTRA_DDA_HLA_I, MS_SPECTRA_DDA_HLA_II, MS_SPECTRA_DIA_HLA_I, MS_SPECTRA_DIA_HLA_II
• The syntax for defining MS_SPECTRA_SAMPLES in the configuration file has been simplified:
• Injections are now grouped by sample (This means that the sample name is written only once, followed by all its associated MS files) as follow: sampleA:ms_file1,ms_file2;sampleB:ms_file3,ms_file4;… Colon ( : ) separates the sample name from its list of MS files. Comma ( , ) separates multiple MS files belonging to the same sample. Semicolon ( ; ) separates different samples
• Removed Comet-NewAnce module: This module was removed due to its limited applicability (restricted to Thermo DDA data). NeoDisc now relies on the FragPipe-based workflow, which supports both Thermo and Bruker data in DDA and DIA modes.
Minor changes:
• Updated proteowizard (msconvert) version in the container (3.0.25182)
• Convert only thermo DIA data to mzML (this conversion is required for DIA-NN). All other MS files are natively supported, saving computing time.
• Spectra are no longer automatically exported to pdf – to save computing time and space. We suggest using pdvviewer to inspect spectra, or load fragpipe results in the fragpipe GUI to inspect and export spectra of interest.
Bug Fixes:
• Fixed a bug preventing the ML algorithm from running properly (version 1.7.1)
• Fixed a bug in the annotation of some MS-identified neoantigens in the list of predictions
• Fixed a bug in the annotation of mutation expression in certain high mutational-load samples
Version 1.7.1
IMPORTANT: WE NOTICED A BUG IN THIS RELEASE. THAT VERSION SHOULD NOT BE USED, PLEASE USE A MORE RECENT VERSION INSTEAD.
Updates:
• Integration of NeoDiscMS workflow as described in:
Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics
Shapiro E. I, Huber F, Michaux J, Bassani-Sternberg M, Nature Communications, 2025, 0.1038/s41467-025-62647-4
• See the description of the workflow and the new configuration file variables in the manual for more information.
• Updated Comet to version: 2024.02_0
• Updated Fragpipe to version: 22.0
• DDA samples are analyzed in DDA+ mode in fragpipe
• Possibility to select which variable (MS_VARIABLE_MODIFICATIONS) and fixed (NEODISCMS_VARIABLE_MODIFICATIONS) modifications to include in the MS analysis. See the description of the configuration file in the manual.
• Sequenza: Updated copy-number estimation (ratio.priority=True) for better performance on WES data
• Various bug fixes
Version 1.7.0 – bugfix 2
Bug Fixes:
• Improvement in the -cleandnafq and -cleanrnafq outputs: support for a wider range of FASTQ sequence identifier formats.
• Addition of light and full modes to -cleandnafq and -cleanrnafq:
• light mode reformats FASTQ read identifiers into a format compatible with GATK and Picard tools.
• full mode performs the same reformatting and also deduplicates reads.
• Fixed a bug affecting the combination of MS-identified peptides when only HLA-I or HLA-II injections were measured, but predicted binders existed for both HLA-I and HLA-II.
Version 1.7.0 – bugfix 1
To enhance the download experience, the resources have been separated from the container. As a result, the installation process has changed slightly, as reflected in the updated Manual. Additionally, a few bugs have been fixed in the Software and Resources.
Bug Fixes:
• Fixed issue with running MS analysis using DIA only.
• Resolved problem when running MS analysis with only HLA-I or HLA-II alleles.
• Corrected underestimation of mutational load when using gencode_v43 as the capture kit.
• Added –no-home and –cleanenv options to the Singularity command to prevent loading environment variables in the container.
• Various minor bug fixes.
Version 1.7.0
First release of NeoDisc, as published in:
A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy
Huber F, et al. Nature Biotechnology, 2024, 10.1038/s41587-024-02420-y