Attributions
| Acknowledging Inferentus |
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We do not require － but very much appreciate － any attribution to our services in your publications and presentations.
Such attribution helps other researchers understand your scientific workflow and helps us survive as a service provider.
The following is an example acknowledgement statement that you can use:
Some of the presented analyses were performed by Inferentus LLC (www.inferentus.com), a data analysis service provider (analysis code XXXXX).
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| Citing 3rd party resources |
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Many of our workflows utilize 3rd party resources such as databases and software. If analyses provided to you by Inferentus use these resources, please give them proper attribution as well.
The following is a non-exhaustive list of resources used in some of our analyses, along with suggested bibliography that you can cite.
For information on which resources are used in any given analysis, please refer to that analysis' introduction page and explanation of results.
SILVA SSU database
- Glöckner, F. O., Yilmaz, P., Quast, C., Gerken, J., Beccati, A., Ciuprina, A. et al. (2017). 25 years of serving the community with ribosomal RNA gene reference databases and tools. Journal of Biotechnology 261:169-176
KOfam HMM database
- Aramaki, T., Blanc-Mathieu, R., Endo, H., Ohkubo, K., Kanehisa, M., Goto, S. et al. (2019). KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36:2251-2252
GenBank database
- Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Sayers, E. W. (2015). GenBank. Nucleic Acids Research 44:D67-D72
eggNOG
- Hernández-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C. P., Giner-Lamia, J., Mende, D. R. et al. (2023). eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research 51:D389-D394
Unite ITS database
- Nilsson, R. H., Larsson, K., Taylor, A. F. S., Bengtsson-Palme, J., Jeppesen, T. S., Schigel, D. et al. (2019). The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research 47:D259-D264
FAPROTAX
- Louca, S., Parfrey, L. W., Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272-1277
Castor R package
- Louca, S., Doebeli, M. (2018). Efficient comparative phylogenetics on large trees. Bioinformatics 34:1053-1055
vsearch
- Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahe, F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584
Prodigal
- Hyatt, D., Chen, G., LoCascio, P. F., Land, M. L., Larimer, F. W., Hauser, L. J. (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119
diamond
- Buchfink, B., Xie, C., Huson, D. H. (2014). Fast and sensitive protein alignment using DIAMOND. Nature Methods 12:59-60
dada2
- Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13:581-583
FastTree
- Price, M. N., Dehal, P. S., Arkin, A. P. (2010). FastTree 2: Approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490
IQtree2
- Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von, H. A. et al. (2020). IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37:1530-1534
HMMER
- Mistry, J., Finn, R. D., Eddy, S. R., Bateman, A., Punta, M. (2013). Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Research 41:e121
MAFFT
- Katoh, K., Standley, D. M. (2014). MAFFT: iterative refinement and additional methods. In Multiple sequence alignment methods. Pages 131--146. Springer
MegaHit
- Li, D., Liu, C., Luo, R., Sadakane, K., Lam, T. (2015). MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674-1676
CheckM2
- Chklovski, A., Parks, D. H., Woodcroft, B. J., Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods 20:1203-1212
Bowtie
- Langmead, B., Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359
GTDB-Tk
- Chaumeil, P., Mussig, A. J., Hugenholtz, P., Parks, D. H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36:1925-1927
FastANI
- Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., Aluru, S. (2018). High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications 9:5114
MIT General Circulation Model
- Marotzke, J., Giering, R., Zhang, K. Q., Stammer, D., Hill, C., Lee, T. (1999). Construction of the adjoint MIT ocean general circulation model and application to Atlantic heat transport sensitivity. Journal of Geophysical Research: Oceans 104:29529-29547
NOAA World Ocean Atlas
- Reagan, R., Garcia, G., Boyer, B., Baranova, B., Bouchard, B., Cross, C. et al. (2024). World Ocean Atlas 2023: Product documentation. Manual
NASA Earth Observations (NEO)
NASA National Snow & Ice Data Center
CheckV
- Nayfach, S., Camargo, A. P., Schulz, F., Eloe-Fadrosh, E., Roux, S., Kyrpides, N. C. (2021). CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature Biotechnology 39:578-585
MetaPhinder
- Jurtz, Vanessa Isabell AND Villarroel, Julia AND Lund, Ole AND Voldby Larsen, Mette AND Nielsen, Morten (2016). MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets. PLOS ONE 11:1-14
VirSorter2
- Guo, J., Bolduc, B., Zayed, A. A., Varsani, A., Dominguez-Huerta, G., Delmont, T. O. et al. (2021). VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9:37
metaViralSpades
- Antipov, D., Raiko, M., Lapidus, A., Pevzner, P. A. (2020). MetaviralSPAdes: assembly of viruses from metagenomic data. Bioinformatics 36:4126-4129
viralVerify
- Antipov, D., Raiko, M., Lapidus, A., Pevzner, P. A. (2020). MetaviralSPAdes: assembly of viruses from metagenomic data. Bioinformatics 36:4126-4129
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