IRMA is a highly configurable next-generation sequencing assembly pipeline for virus genomes. Seed references are refined and edited as reads are matched, sorted, and aligned across virus genomes or gene segments. More information can be found on the IRMA website or you can read the manuscript. If you use IRMA in a paper, please cite us.
Visit the CHANGELOG to see recent changes.
- IRMA - the Iterative Refinement Meta-Assembler
IRMA takes a module-configuration name, one or two fastq, and a project name. The project name can be a full path. For example:
Usage:
(PAIRED-END): IRMA <MODULE|MODULE-CONFIG> <R1.fastq.gz|R1.fastq> <R2.fastq.gz|R2.fastq> [path/to/]<sample_name> [options]
(SINGLE-END): IRMA <MODULE|MODULE-CONFIG> <fastq|fastq.gz> [path/to/]<sample_name> [options]
Options:
--external-config|-c <VALID_CONFIG_PATH>More usage information: https://wonder.cdc.gov/amd/flu/irma/run.html
We recommend a multi-core machine with no fewer than 8 cores (16 or more threads work best) and at least 16 GB of RAM. IRMA runtime is impacted by the number of cores available on a machine. In addition software requirements include:
- Perl 5.16
- R 3.6+
- BASH 3+
- Linux: RHEL 8+ or any recent Ubuntu like Bookworm
- OR macOS 10.14 on intel, macOS 11 on arm64 (Rosetta 2 required for LABEL)
Download the latest archive via our releases page. Use of wget or curl for downloads is recommended for macOS to preserve functionality.
-
Unzip the archive containing IRMA.
-
Move the package to your desired location and add the folder to your
PATH- Note: IRMA_RES and IRMA must be in the same folder.
-
IRMA is now installed. To test it from the package folder, execute:
./IRMA FLU tests/test2.fastq.gz test_project
Simply run:
## From Github
docker run --rm -itv $(pwd):/data ghcr.io/cdcgov/irma:latest IRMA # more args
## From Dockerhub
docker run --rm -itv $(pwd):/data docker/cdcgov/irma:latest LABEL # more argsFor a GUI interface, please visit MIRA. For usage with nextflow consider MIRA-NF. MIRA provides more end-to-end functionality out-of-the-box by integrating other components and providing extra summaries.
We aggregate and provide builds of 3rd party software for execution at runtime with IRMA. Similarly, still more third-party software is co-distributed with LABEL for runtime with IRMA. You may install or obtain your own copies and IRMA will detect them, but the user will be required to test for compatibility.
- blat v35
- Artifacts:
blat - Purpose: match, sort, and rough align phase
- License: noncommerical license (licensed for personal, academic, and non-profit) with permission to redistribute in IRMA
- Artifacts:
- minimap2 v2.29
- Artifacts:
minimap2 - Purpose: final assembly phase
- License: MIT
- Artifacts:
- GNU Parallel v20200422
- Artifacts:
parallel - Requires: system Perl
- Purpose: local parallelization
- License: GPL v3
- Artifacts:
- pigz v2.8
- Artifacts:
pigz - Purpose: zipping FASTQ, but can also use
gzip - License: free to redistribute
- Artifacts:
- samtools v1.21
- Artifacts:
samtools - Purpose: converting SAM to BAM, indexing BAM, sorting BAM
- License: MIT/Expat
- Artifacts:
- SSW v1.2.5M
- Artifacts:
ssw - Custom modifications: https://github.com/sammysheep/Complete-Striped-Smith-Waterman-Library/tree/IRMA%40v1.3
- Purpose: final assembly phase
- License: MIT
- Artifacts:
- GNU Parallel
- SHOGUN version 1.1.0 (2.1+ is not compatible)
- Artifacts:
shogun(cmdline_static) - Exception: apple/arm64 requires Rosetta2
- Purpose: executes the SVM decision phase.
- License: GPL v3
- Artifacts:
- SAM version 3.5
- Artifacts:
align2model,hmmscore,modelfromalign - Purpose: build HMM profiles, score sequences for evaluation
- License: Custom academic/government, not-for-profit, redistributed with permission
- Artifacts:
Warning
Note that blat and SAM (via LABEL) is redistributed with permission but their terms exclude commerical use without a license. If you are a commercial entity, you might need to reach out to the respective authors (see example blat-license and sam-license) to obtain a license for commercial use.
New feature integration is mainly being moved to the irma-core project (supported by Zoe), which is a mandatory component of IRMA as of v1.3.0. The IRMA repo itself will continue to address fixes needed for the Perl, R, and BASH code base, albeit some pieces may be obviated in future versions by IRMA-core or other changes. This repo will also continue to be responsible for data updates and other module artifacts and for the overall build and release.
We elect to define semantic versioning for IRMA explicitly. Some of our choices may differ from other interpretations of SemVer; our have been made for practicality reasons.
- Breaking changes to the command line interface (CLI)
- Breaking changes to data output that are typically processed downstream (tables, FASTA, BAM, etc.)
- Breaking changes to configuration format or changes to a configuration that would cause IRMA to abort
- Breaking changes to supported data inputs
- Adding new, non-breaking features
- Changes that break undocumented/unintended behaviors for generating data without altering output data formats or structure
- Changes in figures or figure generation
- Changes in module or program configuration defaults
- Re-mapping or obviating an existing configuration field without breaking anything defined in Major.
- Changes to the structure of saved, intermediate data (as some people rely on this)
- Bug fixes
- Minor performance improvements
- Non-breaking updates to dependencies
- Log or error improvements
- Changes in config file defaults
- Changes in module data meant to correct a performance or correctness issue
- Removing an experimental configuration field without causing an abort
For direct correspondence on the project, feel free to contact: Samuel S. Shepard, Centers for Disease Control and Prevention or reach out to the IRMA contributors.
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