Profile HMM marker sets

Archaea_76.hmm - (Anvi'o) Lee, https://doi.org/10.1093/bioinformatics/btz188 (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Archaea_76) Bacteria_71.hmm - (Anvi'o) Lee modified, https://doi.org/10.1093/bioinformatics/btz188 (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Bacteria_71) Protista_83.hmm - (Anvi'o) Delmont, http://merenlab.org/delmont-euk-scgs (https://github.com/merenlab/anvio/tree/master/anvio/data/hmm/Protista_83) Fungi_593.hmm - (FGMP) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2782-9 CPR_43.hmm - (CheckM) https://github.com/Ecogenomics/CheckM/tree/master/custom_marker_sets eukaryota_odb10 - (BUSCO) https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2020-09-10.tar.gz <strong>Citation:</strong> * Espinoza, J.L., Dupont, C.L. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics 23, 419 (2022). https://doi.org/10.1186/s12859-022-04973-8 * Espinoza, Josh (2022): Profile HMM marker sets. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19616016.v1 * Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. 2015. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3:e1319 https://doi.org/10.7717/peerj.1319 * Cissé, O.H., Stajich, J.E. FGMP: assessing fungal genome completeness. BMC Bioinformatics 20, 184 (2019). https://doi.org/10.1186/s12859-019-2782-9 * Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. * Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021 Sep 27;38(10):4647-4654. doi: 10.1093/molbev/msab199.