Page 85 - Read Online
P. 85

Page 16 of 16                  Renzi et al. Microbiome Res Rep 2024;3:2  https://dx.doi.org/10.20517/mrr.2023.27

               132.      Edgar RC, Flyvbjerg H. Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics
                    2015;31:3476-82.  DOI  PubMed
               133.      Truong DT, Franzosa EA, Tickle TL, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 2015;12:902-
                    3.  DOI
               134.      Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 2019;20:257.  DOI  PubMed  PMC
               135.      Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015;12:59-60.  DOI  PubMed
               136.      Olson ND, Treangen TJ, Hill CM, et al. Metagenomic assembly through the lens of validation: recent advances in assessing and
                    improving the quality of genomes assembled from metagenomes. Brief Bioinform 2019;20:1140-50.  DOI  PubMed  PMC
               137.      Jünemann S, Kleinbölting N, Jaenicke S, et al. Bioinformatics for NGS-based metagenomics and the application to biogas research. J
                    Biotechnol 2017;261:10-23.  DOI
               138.      Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res
                    2017;27:824-34.  DOI  PubMed  PMC
               139.      Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics
                    assembly via succinct de Bruijn graph. Bioinformatics 2015;31:1674-6.  DOI
               140.      Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly
                    uneven depth. Bioinformatics 2012;28:1420-8.  DOI
               141.      Kang DD, Li F, Kirton E, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from
                    metagenome assemblies. PeerJ 2019;7:e7359.  DOI  PubMed  PMC
               142.      Alneberg J, Bjarnason BS, de Bruijn I, et al. Binning metagenomic contigs by coverage and composition. Nat Methods 2014;11:1144-
                    6.  DOI
               143.      Wu YW, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic
                    datasets. Bioinformatics 2016;32:605-7.  DOI  PubMed
               144.      Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome
                    2018;6:158.  DOI  PubMed  PMC
               145.      Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30.  DOI  PubMed  PMC
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