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Citation and references

Use this page when you publish results from FunFlux. It gives the reference for FunFlux itself and for the v1 workflows. It then lists, stage by stage, the tools and databases a run can use, with their versions and the numbers of their references. The page ends with the acknowledgements, the full list of references and the works cited on Validation on public genomes.

Terms used on this page
concept DOI the Zenodo DOI shared by all versions of a record, which always leads to the newest; each version also has a DOI of its own
contig filter rule filter_contigs: on SPAdes-style headers it drops contigs under 500 bp or 2x coverage; other headers are only cut at their first space or tab
mitochondrion screen rule screen_mitochondria, part of the contamination and mitochondrion screen: it confirms mitochondrial contigs from BLAST hits to mitochondrial genomes and, in the long-read modes, the assembler's evidence
contig selector rule select_contigs, the last step of the screen: it keeps or removes each contig by genus, as parameters.decontamination says; the default, off, keeps every contig
ITS window the stretch cut around one 5.8S gene, 2,000 bp on each side by default, turned to read from SSU to LSU before ITSx runs
contig summary the table 02.assembly/{sample}/eval/contig_summary.tsv: one row per contig of the draft, with its evidence (telomeres, depth, rDNA units, genes) and a verdict
AMR screen the optional resistance-mutation screen, off by default (parameters.amr.chroquetas), in which ChroQueTas looks in each genome for the changes FungAMR lists for the species
funannotate database the frozen snapshot of funannotate's data, such as Swiss-Prot, Pfam, the BUSCO set and stored AUGUSTUS models, downloaded once from Zenodo into directories.funannotate_db

Citing FunFlux

Antonielli, L., & Brader, G. (2026). FunFlux: Integrated workflow for fungal genome assembly and annotation (v2.1.0). Zenodo. https://doi.org/10.5281/zenodo.13612159

The DOI 10.5281/zenodo.13612159 is the concept DOI, which always resolves to the newest version. Each release also has a version DOI of its own on Zenodo. Cite the version DOI when the exact code matters.

The repository is https://github.com/iLivius/FunFlux, and the documentation is at https://iLivius.github.io/FunFlux/. FunFlux is released under the MIT License. See Licensing.

The contig filter, the mitochondrion screen, the contig selector and the ITS windows have no tool of their own to cite, so cite FunFlux for them. The contig filter of contigs mode, the contig selector and the layout of the workflow come from BacFlux, which is also released under the MIT License.

For the contig summary, tidk does the telomere search, so cite tidk with FunFlux. The papers behind FunFlux's table of telomere repeat units are listed in the Contig summary rows under Tools and databases.

The ChroQueTas authors ask to be cited through the FungAMR paper

The AMR screen runs ChroQueTas. As the ChroQueTas authors ask, cite FungAMR and ChroQueTas through the FungAMR paper (Bédard et al. 2025). Cite the tools ChroQueTas runs as well, which are listed in the AMR screen rows under Tools and databases.

Results from a v1 workflow

If a v1 workflow produced your results, cite the record of the version you ran:

Workflow Version (published) DOI
FunFlux 1.0.3 (2024-08-30) 10.5281/zenodo.13612160
FunFlux 1.0.4 (2025-06-08) 10.5281/zenodo.15618338
FunFlux 1.0.5 (2026-01-24) 10.5281/zenodo.18363368
FunFlux 1.0.6 (2026-01-31) 10.5281/zenodo.18445164
FunFlux 1.0.7 (2026-02-02) 10.5281/zenodo.18455939
FunFlux 1.1.0 (2026-06-18) 10.5281/zenodo.20749375
Funnotator shipped inside FunFlux 1.x the DOI of the FunFlux release it came with
FunFluxL 0.1.0 (2026-06-22) 10.5281/zenodo.20796645; concept DOI 10.5281/zenodo.20796644
FunFluxL+ never released none

Tools and databases

Cite the tools and databases your run used, as well as FunFlux. Which rows apply depends on the mode, the read type and the settings of your run. The versions are those FunFlux 2.1.0 installs or, for the tools you install yourself, those it was tested with. The numbers in the last column point to the list under References.

Stage Tool or database References
Workflow Snakemake (9.14.6) 54
Reads and assembly, illumina Bowtie 2 (2.5.4) for PhiX removal and read mapping, with SAMtools (1.21) 41, 42, 24
fastp (1.0.1) 18, 19, 20
SPAdes (4.2.0) 60
Qualimap (2.3) 56
Reads and assembly, longread fastplong (0.7.1), ONT adapter trimming; its author asks users to cite fastp until fastplong has a paper of its own 18
Filtlong (0.3.1) 77
NanoPlot (1.46.2) 25
hifiasm (0.25.0), the default assembler 21, 22, 23
Flye (2.9.6), the alternative assembler 38
minimap2 (2.30) and SAMtools (1.21) for read mapping, Qualimap (2.3) 45, 46, 24, 56
Medaka (2.2.2), ONT samples only 57
Reads and assembly, hybrid the illumina and longread tools above as above
Polypolish (0.6.1) with BWA (0.7.19) 78, 9, 44
Contig self-mapping, contigs with the screen minimap2 (2.30) and SAMtools (1.21) 45, 46, 24
Contamination screen BLAST+ (2.16.0), megablast against NCBI core_nt 14, 55, 80
BlobTools (1.1.1) 40
Adapter screen BLAST+ (2.16.0), blastn-short, against the adapters and barcodes of the Oxford Nanopore Chemistry Technical Document (CHTD_500_v1_revAV_24July2026), the PacBio and MGI records of NCBI UniVec (the file of 21 August 2024) and the Illumina records of UniVec build 10.1 14
Assembly QC QUAST (5.3.0) 53
BUSCO (6.0.0) with the odb12 lineage datasets, finding the genes with miniprot (0.18) 72, 47
Contig summary tidk (0.3.0): tidk explore lists the tandem repeat units of the contig ends, tidk ends calls the arrays of every candidate unit 12
the tidk telomere repeat database (telo_database_v2.tsv, downloaded from the address in links.telomere_db_link) 12
FunFlux's own scripts; the telomere repeat units of the fungal groups 49, 71, 16, 52, 65, 11, 27, 43, 10
the two databases that list a species' repeat: TeloBase and the Telomerase Database 50, 59
ITS taxonomy nhmmer from HMMER (3.4), with the 5.8S profiles of ITSx 76
ITSx (1.1.3) 6
SINTAX in VSEARCH (2.30.0) 26, 64
UNITE release for eukaryotes 19.02.2025 2, 1
Repeat masking tantan (51), the default 30
RepeatModeler (2.0.8) and RepeatMasker (4.2.3) 29, 68
Gene prediction funannotate (1.8.17): clean, sort, predict; clean finds duplicated contigs with minimap2 (2.31) 58, 45, 46
AUGUSTUS (3.5.0) 69, 70
SNAP (2017_03_01) 39
GlimmerHMM (3.0.4) 51
Tiberius (1.1.8), on by default, with its authors' fungi model 31
BUSCO dikarya_odb9 set of the funannotate database, on which SNAP and GlimmerHMM are trained none: the BUSCO site names a paper only for odb10 and odb12 datasets
EVidenceModeler (1.1.1) 34
tRNAscan-SE (2.0.13) 17
DIAMOND (2.2.4) and Exonerate (2.4.0), aligning your protein FASTA and UniProtKB/Swiss-Prot to the genome 13, 67, 75
GeneMark-ES (optional) 48, 73
Functional annotation InterProScan (5.78-109.0), with InterPro and Pfam 36, 8
eggNOG-mapper (2.1.13) with DIAMOND (2.0.15), against eggNOG 5.0.2 15, 13, 35
antiSMASH (8.0.4) 7
SignalP 6.0 (optional) 74
funannotate annotate (1.8.17) with the databases held in the funannotate database: UniProtKB/Swiss-Prot 2026_03, Pfam 38.2, MEROPS 12.5, dbCAN (HMMdb V11), Gene Ontology, MIBiG 1.4 58, 75, 8, 62, 81, 3, 32, 79
AMR screen (optional, off by default) ChroQueTas (1.0.1) with its FungAMR database (db-v20250811) 5, 61
miniprot (0.14), BLAST+ (2.16.0) blastp, MAFFT (7.525), SeqKit (2.1.0) and EMBOSS (6.6.0) seqret: the tools ChroQueTas runs 47, 14, 37, 66, 63
the intron after codon 143 of cytochrome b, in the worked example on B05.10 4, 33
Report MultiQC (1.33) 28

The DOI of the funannotate database fixes the versions of the databases in it

The funannotate database, funannotate_db_1.8.17_2026-10-08, has the DOI 10.5281/zenodo.23265189, which fixes the versions of the databases in it. It holds MIBiG 1.4 data, while reference 79 is the current MIBiG paper. See Reference databases.

Acknowledgements

This work was supported by the RATION project (Risk AssessmenT InnOvatioN for low-risk pesticides), funded by the European Union's Horizon Europe research and innovation programme under grant agreement No. 101084163.

Much of v2.0.0 — merging FunFlux 1.x, Funnotator and FunFluxL into one workflow, adding the hybrid mode and writing this documentation — was done with Claude Code. Anthropic provided six months of Claude Max through their Open Source programme, and the scale of the v2 rewrite would not have been realistic without it.

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References of the validation page

Validation on public genomes cites these works besides the tools above. On that page, Liftoff, gffread and gffcompare compared FunFlux's genes with the reference. These three tools are not part of FunFlux.

  • Liu, M., et al. (2026). A chromosome-scale nuclear genome and complete mitogenome of the bio-control fungus Cordyceps cateniannulata. Scientific Data, 13, 871. https://doi.org/10.1038/s41597-026-07231-1 (the reference genome assembly ASM5650595v1, GenBank GCA_056505955.1)
  • Pertea, G., & Pertea, M. (2020). GFF Utilities: GffRead and GffCompare. F1000Research, 9, ISCB Comm J-304. https://doi.org/10.12688/f1000research.23297.2 (gffread 0.12.9, gffcompare 0.12.10)
  • Shumate, A., & Salzberg, S. L. (2021). Liftoff: accurate mapping of gene annotations. Bioinformatics, 37(12), 1639–1643. https://doi.org/10.1093/bioinformatics/btaa1016 (Liftoff 1.6.3)
  • Tiberius fungi model: its parameter file model_cfg/fungi.yaml (it dates the model 2026-02-06; the model file FunFlux downloads is of 8 February 2026; weights trained by K. Hoff), which lists the species used for training, validation and testing; Botrytis cinerea is among the training species, no Cordyceps species is, and Akanthomyces muscarius and Beauveria bassiana are its only training species of the family Cordycipitaceae. https://github.com/Gaius-Augustus/Tiberius/blob/0db79a92ab78037a636439d7b880ac942e931084/model_cfg/fungi.yaml
  • Van Kan, J. A., et al. (2017). A gapless genome sequence of the fungus Botrytis cinerea. Molecular Plant Pathology, 18(1), 75–89. https://doi.org/10.1111/mpp.12384 (the reference genome assembly ASM14353v4, RefSeq GCF_000143535.2)