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CITATION_NOTICE
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If you use lsaBGC, please cite: https://www.biorxiv.org/content/10.1101/2022.04.20.488953v2
lsaBGC is made possible by many other tools including:
- BGC prediction software (can vary but please cite appropriately):
- antiSMASH: https://academic.oup.com/nar/article/49/W1/W29/6274535
- GECCO (still under review): https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1
- DeepBGC: https://academic.oup.com/nar/article/47/18/e110/5545735
- Phylogeny construction & diversity estimation:
- GToTree: https://academic.oup.com/bioinformatics/article/35/20/4162/5378708
- MASH: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
- Ortholog group identification:
- OrthoFinder2: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1832-y
- SonicParanoid2 (still under review): https://www.biorxiv.org/content/10.1101/2023.05.14.540736v1
- General processing of sequencing data and phylogenies:
- biopython: https://academic.oup.com/bioinformatics/article/25/11/1422/330687
- ete3: https://academic.oup.com/mbe/article/33/6/1635/2579822
- Gene calling:
- prodigal: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119
- pyrodigal: https://joss.theoj.org/papers/10.21105/joss.04296
- If using BiG-SCAPE for clustering BGCs into GCFs or if you use CORASON to visually explore
the context of multi-GCF homolog groups highlighted:
- BiG-SCAPE/CORASON: https://pubmed.ncbi.nlm.nih.gov/31768033/
- Annotation databases:
- KOfam HMMs: https://academic.oup.com/bioinformatics/article/36/7/2251/5631907
- PGAP HMMs: https://pubmed.ncbi.nlm.nih.gov/27342282/
- MIBiG DB: https://academic.oup.com/nar/article/51/D1/D603/6833236
- Protein alignment and profile HMM construction:
- MAFFT: https://academic.oup.com/mbe/article/30/4/772/1073398
- MAGUS (no longer used since v1.37): https://academic.oup.com/bioinformatics/article/37/12/1666/6012350
- MUSCLE: https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full
- Visualization software:
- ggplot2: https://ggplot2-book.org/
- ggtree: https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12628
- gggeenes: https://github.com/wilkox/gggenes
- cowplot: https://wilkelab.org/cowplot/articles/plot_grid.html
- iTol: https://pubmed.ncbi.nlm.nih.gov/30931475/
- Identification of additional GCF instances:
- DIAMOND: https://www.nature.com/articles/nmeth.3176
- HMMER: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002195
- pomegranate: https://www.jmlr.org/papers/volume18/17-636/17-636.pdf
- Metagenomics analysis in lsaBGC-DiscoVary:
- Bowtie2: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381/
- DESMAN: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1309-9