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               REFERENCES
               1.       Comin M, Di Camillo B, Pizzi C, Vandin F. Comparison of microbiome samples: methods and computational challenges. Brief
                   Bioinform 2021;22:88-95.  DOI  PubMed
               2.       Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-10.  DOI
                   PubMed
               3.       Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P. Compareads: comparing huge metagenomic experiments. BMC
                   Bioinformatics 2012;13:S10.  DOI  PubMed  PMC
               4.       Maillet N, Collet G, Vannier T, Lavenier D, Peterlongo P. Commet: comparing and combining multiple metagenomic datasets. In:
                   2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 2014 Nov 2-5; Belfast, UK. IEEE; 2015. p. 94-8.
                   DOI
               5.       Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG. Assessment of k-mer spectrum applicability for metagenomic
                   dissimilarity analysis. BMC Bioinformatics 2016;17:38.  DOI  PubMed  PMC
               6.       Wu YW, Ye Y. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J Comput Biol 2011;18:523-
                   34.  DOI  PubMed  PMC
               7.       Fofanov Y, Luo Y, Katili C, et al. How independent are the appearances of n-mers in different genomes? Bioinformatics
                   2004;20:2421-8.  DOI  PubMed
               8.       Ondov BD, Treangen TJ, Melsted P, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol
                   2016;17:132.  DOI  PubMed  PMC
               9.       Choi I, Ponsero AJ, Bomhoff M, Youens-Clark K, Hartman JH, Hurwitz BL. Libra: scalable k-mer-based tool for massive all-vs-all
                   metagenome comparisons. Gigascience 2019;8:giy165.  DOI  PubMed  PMC
               10.      Benoit G, Peterlongo P, Mariadassou M, et al. Multiple comparative metagenomics using multiset k-mer counting. PeerJ Comput Sci
                   2016;2:e94.  DOI
               11.      Gourlé H, Karlsson-Lindsjö O, Hayer J, Bongcam-Rudloff E. Simulating Illumina metagenomic data with InSilicoSeq. Bioinformatics
                   2019;35:521-2.  DOI  PubMed  PMC
               12.      Yu Z, Du F, Ban R, Zhang Y. SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles.
                   BMC Bioinformatics 2020;21:331.  DOI  PubMed  PMC
               13.      Li W, O'Neill KR, Haft DH, et al. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model
                   curation. Nucleic Acids Res 2021;49:D1020-8.  DOI  PubMed  PMC
               14.      Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci 2003;14:927-30.  DOI
               15.      Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 2019;20:257.  DOI  PubMed  PMC
               16.      Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci
                   2017;3:e104.  DOI
               17.      Benoit G, Mariadassou M, Robin S, Schbath S, Peterlongo P, Lemaitre C. SimkaMin: fast and resource frugal de novo comparative
                   metagenomics. Bioinformatics 2020;36:1275-6.  DOI  PubMed
               18.      Matharu D, Ponsero AJ, Dikareva E, et al. Bacteroides abundance drives birth mode dependent infant gut microbiota developmental
                   trajectories. Front Microbiol 2022;13:953475.  DOI  PubMed  PMC
               19.      Hiseni P, Rudi K, Wilson RC, Hegge FT, Snipen L. HumGut: a comprehensive human gut prokaryotic genomes collection filtered by
                   metagenome data. Microbiome 2021;9:165.  DOI  PubMed  PMC
               20.      Rowe WP, Carrieri AP, Alcon-Giner C, et al. Streaming histogram sketching for rapid microbiome analytics. Microbiome 2019;7:40.
                   DOI  PubMed  PMC
               21.      Pierce NT, Irber L, Reiter T, Brooks P, Brown CT. Large-scale sequence comparisons with sourmash. F1000Res 2019;8:1006.  DOI
                   PubMed  PMC
               22.      Murray KD, Webers C, Ong CS, Borevitz J, Warthmann N. kWIP: The k-mer weighted inner product, a de novo estimator of genetic
                   similarity. PLoS Comput Biol 2017;13:e1005727.  DOI  PubMed  PMC
               23.      Fimereli D, Detours V, Konopka T. TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data.
                   Nucleic Acids Res 2013;41:e86.  DOI  PubMed  PMC
               24.      Ulyantsev VI, Kazakov SV, Dubinkina VB, Tyakht AV, Alexeev DG. MetaFast: fast reference-free graph-based comparison of
                   shotgun metagenomic data. Bioinformatics 2016;32:2760-7.  DOI  PubMed
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