IRMA is used for NGS virus sequence assembly; in particular, for influenza, RSV and SARS-CoV-2.
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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.
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
Simply run:
## From Github
docker run --rm -itv $(pwd):/data ghcr.io/cdcgov/irma:latest IRMA # more args
## From Dockerhub
docker run --rm -itv $(pwd):/data docker.io/cdcgov/irma:latest IRMA # more args
ghcr.ioWhile we publish to both ghcr.io and Docker Hub, please use the former for
cryptographic verification of the image signature and SLSA build provenance
attestation. Verification with Sigstore cosign:
# Replace with the version of interest
TAG=latest
cosign verify --new-bundle-format ghcr.io/cdcgov/irma:$TAG \
--certificate-oidc-issuer https://token.actions.githubusercontent.com \
--certificate-identity-regexp '^https://github[.]com/CDCgov/irma/[.]github/workflows/release[.]yml@refs/tags/.+$'
cosign verify-attestation --new-bundle-format --type slsaprovenance1 \
ghcr.io/cdcgov/irma:$TAG \
--certificate-oidc-issuer https://token.actions.githubusercontent.com \
--certificate-identity-regexp '^https://github[.]com/CDCgov/irma/[.]github/workflows/release[.]yml@refs/tags/.+$'
For 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.
blatminimap2parallelpigzgzipsamtoolssswshogun (cmdline_static)align2model, hmmscore, modelfromalignWarning
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.
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.
This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later. This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version. This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details. You should have received a copy of the Apache Software License along with this program. If not, see: http://www.apache.org/licenses/LICENSE-2.0.html. The source code forked from other open source projects will inherit its license.
This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer. For more information about CDC's privacy policy, please visit http://www.cdc.gov/other/privacy.html.
Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.
All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.
This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.
Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.
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docker pull cdcgov/irma