Welcome to the LENS documentation!
LENS (Landscape of Effective Neoantigens Software) is a tumor antigen discovery workflow.
Instructions for installing RAFT, the Nextflow-based workflow manager that runs LENS, are available at Installing RAFT.
A demonstration of LENS can be run using the instructions at Demonstration.
A tutoral for running LENS is available at Usage.
An overview of LENS outputs is available at LENS Outputs.
A description of the LENS report can be found at LENS Report.
Frequently Asked Questions and their answers can be found at Frequently Asked Questions.
Information regarding technical details of the workflow can be found at Technical Details.
The change log is available at Changelog.
The authors of RAFT can be contacted using:
Contents
- Introduction
- Installing RAFT
- Demonstration
- Manifest
- Usage
- Running Off-the-shelf LENS
- Running Off-the-shelf LENS with Mouse Data
- Running Off-the-shelf LENS using cloud service providers (EXPERIMENTAL)
- Running Off-the-shelf LENS with User-defined Parameters
- Running Off-the-shelf LENS with User-specified References
- Running Off-the-shelf LENS with User-specified Tools
- Filesystem Storage Management
- LENS Outputs
- LENS Report
- LENSTools
- Frequently Asked Questions
- What is LENS?
- What antigen sources are supported?
- What is RAFT? How is it different from LENS?
- What input files are required?
- What sequencing technologies are supported?
- How can I run LENS with my own reference files?
- How can I run LENS using different tools?
- How do I know which tool versions are running?
- How do I know which Docker iamge tools are running?
- How do I change which tool versions are used?
- How do I change resource allocations for each tool?
- How is the workflow code in LENS executed?
- How is CTA gene list defined?
- Why are some of my CTA transcripts expressed in normal tissues?
- What do the mTEC columns mean?
- How is ERV list defined?
- How is CCF calculated?
- How is the priorization score calculated?
- How are SNV and InDel peptides generated?
- How should I interpret the LENS report?
- How do I determine how many pMHCs are filtered at each step of LENS?
- Technical Details
- Off-the-shelf defaults
- LENS workflow flowchart
- Somatic Nucleotide Variants (SNVs)
- Variant calling
- Variant filtering
- Variant combining
- Variant annotation
- Filtering variants for expression
- Phasing variants with read-backed phasing
- Creating variant-specific VCFs
- Creating variant-specific, transcript-specific sequences
- Creating SNV-derived peptides
- Calculating binding affinity and presentation score
- Peptide quantification using RNA reads
- Shortcomings and caveats
- Design decisions
- Notes
- Technical
- Somatic Insertion and Deletion Variants (InDels)
- Splice Variants
- Fusion Events
- Endogenous Retroviruses (ERVs)
- Viruses
- Cancer-testis Antigens (CTAs)
- Reference generation notes
- Using NetMHC tools in LENS
- Changelog