IRMA-core is suite of subcommands for both stand-alone and integrated use with IRMA for select portions of the virus sequence assembly process. Processes integrated with IRMA are subject to more rapid internal revision and change while stand-alone processes will attempt to avoid breaking CLI changes where possible. More primitive bioinformatic functionality in IRMA-core can sometimes be pushed down to The Zoe Anthology library for general use cases (PRs welcomed).
This binary compiles using Rust nightly.
| Process | Description | Usage |
|---|---|---|
trimmer |
Used for removing adapters, barcodes, and primers among other things. Read the docs. | irma-core trimmer --help |
| Process | Description | Usage |
|---|---|---|
qc-trim-deflate |
Performs all-in-one FastQ quality control, trimming, and deflation to XFL and FASTA formats. Similar to trimmer. |
irma-core qc-trim-deflate --help |
fastq-converterø |
Performs FastQ quality control, file conversions, and adapter trimming. | irma-core fastq-converter --help |
merge-sam† |
Merges Illumina paired-end reads with parsimonious error correction and detection | irma-core merge-sam --help |
xflate† |
Deflates FastQ files to deduplicated Fasta files, or reinflates deduplicated Fasta files to FastQ files. | irma-core xflate --help |
num-procs |
Provides the physical or logical cores of a CPU portably. | irma-core num-procs --help |
For compatibility notes between IRMA-core and IRMA, see the version matrix.
† May be combined into a future process, deprecated and removed.
ø Deprecated, will be removed.
The correct version of IRMA-core will ship with IRMA and is packaged in all releases since v1.1.0. IRMA-core became non-optional in IRMA v1.3 and later. You can also download IRMA-core for standalone use cases from the IRMA-core release page.
To compile and install IRMA-core yourself, first install rustup, and then:
rustup toolchain install nightly
git clone https://github.com/CDCgov/irma-core
cd irma-core
cargo +nightly b -r
# Install here:
ls -l target/release/irma-coreOne can cite the IRMA manuscript in general, but a software citation of IRMA-core specifically is also possible for stand-alone use cases. We include some citations for convenience in CITATION.bib).
IRMA packages other binaries and that affects its license. IRMA-core is an indendent project from IRMA and so can use more flexible licensing.
No, IRMA contains data + code/binary + configuration that are appropriate for use in that repository. However, in the future it is possible IRMA-core could eliminate dependence on components and make IRMA easier to use and maintain.
In no particular order:
- Retire technical debt and make the IRMA project more maintainable going forward.
- Increase IRMA's portability to systems like Windows.
- Eliminate unneeded dependencies and components.
- Relax licensing for IRMA itself (see above).
- Accelerate execution and/or reduce memory pressure within IRMA.
- Ease the integration of modern features.
- Provide stand-alone functionality outside of IRMA.
For direct correspondence on the project, feel free to contact: Samuel S. Shepard, Centers for Disease Control and Prevention or reach out to other contributors.
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