IRMA: Iterative Refinement Meta-Assembler
IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza, ebolavirus and coronavirus. IRMA is free to use and parallelizes computations for both cluster computing and single computer multi-core setups.
Please refer to our FAQ below or CONTACT US for further questions (do not contact CDC WONDER). The IRMA manuscript provides more background on the methodology.
Please read IRMA's full license and disclaimer.
NOTE: the SAM binaries packaged within LABEL and the BLAT binaries packaged within IRMA may be used for government and/or academic use only. Commercial use and redistribution of SAM or BLAT is excluded without permission from their authors. Please read the SAM license and BLAT license.
- For container users, get the latest IRMA image on Dockerhub
- IRMA v1.2.0 with LABEL v0.6.5 for Linux & MacOS, 08-2024 NEW!
- IRMA v1.1.4 with LABEL v0.6.4 for Linux & MacOS, 02-2024
- IRMA v1.1.3 with LABEL v0.6.4 for Linux & MacOS, 11-2023
- Artificial H3N2 mixtures. Demultiplexed reads for replicates one, two, and three.
| Module | Target Organisms & Types | Notes |
|---|---|---|
| FLU | FLU A & B | |
| CoV | MERS-CoV & SARS-CoV-2 | |
| RSV | RSV_BD, RSV_AD, RSV_B, & RSV_A | Available since v1.2.0; Acknowledgements |
| EBOLA | EBOV_BDBV, CIEBOV, MARV, REBOV, SEBOV, ZEBOV, & LLOV | |
| FLU_AD | FLU A, B, C, & D |
Frequently asked questions
- How do I install IRMA?
- How do I run IRMA?
- What is an IRMA module?
- How are basic calculations carried out?
- How do I customize the configuration files?
- What does the IRMA output look like?
- What is primary versus secondary data?
- What are residual and secondary assemblies?
- How does phase assignment work?
- What options and rules exist for the consensus?
Used by IRMA
- BLAT for the match step
- LABEL, which also packages certain resources used by IRMA:
- Sequence Alignment and Modeling System (SAM) for both the rough align and sort steps
- Shogun Toolbox, which is an essential part of LABEL, is used in the sort step
- SSW for the final assembly step, download our minor modifications to SSW
- MINIMAP2 for the final assembly step (alternate option that may be useful for long read assemblies).
- samtools for BAM-SAM conversion as well as BAM sorting and indexing
- GNU Parallel for single node parallelization
Return to the Influenza Division Bioinformatics Team homepage