ASM 2025 Poster

American Society of Microbiology 2025 Poster References

• metaSPAdes (metagenomic assembler)
  Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017 May;27(5):824–834. doi:10.1101/gr.213959.116

• MetaBAT 2 (Kang et al., 2019)
  Kang D.D., Li F., Kirton E., Thomas A., Egan R., An H., Wang Z. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7:e7359. doi:10.7717/peerj.7359

• BASALT (Qiu et al., 2024)
  Qiu Z., Yuan L., Lian C.-A., et al. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nature Communications 15:2179. doi:10.1038/s41467-024-46539-7

• MaxBin 2 (Wu et al., 2016)
  Wu Y.-W., Simmons B.A., Singer S.W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32(4): 605–607. doi:10.1093/bioinformatics/btv638

• CheckM2 (Chklovski et al., 2023)
  Chklovski A., Parks D.H., Woodcroft B.J., et al. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods 20: 1203–1212. doi:10.1038/s41592-023-01940-w

• dRep (Olm et al., 2017)
  Olm M.R., Brown C.T., Brooks B., Banfield J.F. dRep: a tool for fast and accurate genomic comparisons… ISME Journal 11: 2864–2872. doi:10.1038/ismej.2017.126

• GTDB‑Tk (Chaumeil et al., 2020)
  Chaumeil P.-A., Mussig A.J., Hugenholtz P., Parks D.H. GTDB‑Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36(6): 1925–1927. doi:10.1093/bioinformatics/btz848

• CoverM (Aroney et al., 2025)
  Aroney S.T.N., Newell R.J.P., Nissen J.N., Camargo A.P., Tyson G.W., Woodcroft B.J. CoverM: read alignment statistics for metagenomics. Bioinformatics 41(4):… btaf147. doi:10.1093/bioinformatics/btaf147

• Prodigal (Hyatt et al., 2010)
  Hyatt D., Chen G.-L., LoCascio P.F., et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi:10.1186/1471-2105-11-119

• WGCNA (Langfelder & Horvath, 2008)
  Langfelder P., Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559. doi:10.1186/1471-2105-9-559

• METABOLIC-G (Zhou et al., 2022)
  Zhou Z., Tran P.Q., Breister A.M., et al. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 10:33. doi:10.1186/s40168-021-01213-8

• SPAdes (core algorithm) (Bankevich et al., 2012)
  Bankevich A., Nurk S., Antipov D., et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19(5): 455–477