ImmunoTyper
A Immunoglobulin Heavy Chain Variable Gene genotyping and CNV analysis tool for WGS PacBio Long Reads using ILP Optimization.
Dependencies:
- Poa
- SPOA
- Biopython
- Dense Subgraph Finder from the IG Repertoire Constructor Toolset
- Gurobi via the gurobipy package
- Minimap2
- Blasr (easiest to install via Conda)
Running ImmunoTyper:
ImmunoTyper is run from the src/immunotyper.py
script via the command python immunotyper.py
.
``` usage: immunotyper.py [-h] [–dsf DSF] [–poa POA] [–spoa SPOA] [–minimap MINIMAP] [–blasr BLASR] [–max_copy MAX_COPY] [–debug_log_path DEBUG_LOG_PATH] [–no_coverage_estimation] [–skip_extraction] reads_path expected_coverage output_dir
ImmunoTyper: IGHV Genotyping using PacBio Long Reads
positional arguments: reads_path Input FASTA file of PacBio reads expected_coverage Sequencing depth output_dir Path to output directory. The directory must exist. A fasta is created for each allele call containing the subreads assigned to that call
optional arguments: -h, –help show this help message and exit –dsf DSF Path to Dense Subgraph Finder tool (usually located in ig_repertoire_constructor/dense_subgraph_finder.py) –poa POA Path to POA tool (usually located at poaV2/poa). Default location is ../tools/poaV2/poa. –spoa SPOA Path to SPOA tool (usually located at spoa/build/bin/spoa). Default location is ../tools/spoa/build/bin/spoa –minimap MINIMAP Path to minimap tool –blasr BLASR Path to blasr tool –max_copy MAX_COPY Maximum number of allele copies to call –debug_log_path DEBUG_LOG_PATH Path to write log –no_coverage_estimation Disables empirical coverage –skip_extraction Disables extractinbg subreads from input FASTA reads. Used when subreads have already been isolated (i.e. in simulated data)