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References and Citations

This page tracks citation guidance for Mycelia and the third-party tools it wraps. If a workflow uses external tools or datasets, cite both Mycelia and the tools.

Citing Mycelia

Mycelia does not yet ship a formal paper reference. Until then:

  • Cite the GitHub repository and the specific release tag or commit used.
  • If you mint a DOI for a release, add it here and cite the DOI in publications.

Third-Party Tools (cite when used)

Below is a non-exhaustive list of external tools wrapped by Mycelia. Use the recommended citation from each tool's documentation or manuscript.

  • Assemblers: MEGAHIT, metaSPAdes, SPAdes, Flye/metaFlye, hifiasm, Canu, SKESA, Unicycler
  • Assembly pipelines: Autocycler (https://github.com/rrwick/Autocycler)
  • Annotation: Prodigal, Pyrodigal, Prodigal-gv, Augustus, MetaEuk, BLAST+, MMSeqs2, TransTerm, tRNAscan-SE, MLST
  • QC and validation: fastp, Filtlong, Trim Galore, QUAST, BUSCO, CheckM/CheckM2, MUMmer
  • Alignment and mapping: minimap2, samtools, Qualimap, BWA
  • Variant calling and evaluation: GATK, FreeBayes, Clair3, BCFtools, RTG vcfeval
  • Comparative genomics: Mash, PGGB, cactus, odgi, PanTools (https://github.com/BioinformaticsLab/pantools)
  • Graph construction and k-mer utilities: BCALM (https://github.com/GATB/bcalm), GGCAT (https://github.com/algbio/ggcat), Prokrustean (https://github.com/KoslickiLab/prokrustean)
  • Read simulation: ART, PBSim, DeepSimulator, Badread
  • Structure search and clustering: Foldseek (https://github.com/steineggerlab/foldseek)
  • Taxonomy and profiling: MetaPhlAn, Metabuli, Sylph, Kraken-style tools (planned)
  • Binning: MetaBAT2, VAMB, TaxVAMB, Taxometer, MetaCoAG, GenomeFace, COMEBin, dRep, MAGmax
  • Data access: NCBI datasets, Entrez, SRA Toolkit
  • Infrastructure: SLURM, rclone, Bioconda/conda

Pending Citations

The following components have placeholders in the code and still need formal citations:

  • Wang J., Wang W. (WW5 reduced amino acid alphabet) in src/constants.jl
  • Melo F., Marti-Renom M.A. (MM5 reduced amino acid alphabet) in src/constants.jl

If you can provide the correct references for these items, add them here and replace the placeholders in src/constants.jl.