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      anneng 最后由 编辑

      16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis
      https://www.nature.com/articles/s41598-022-07995-7
      When we used DADA2 for sequence denoising on the full rRNA operon, the biological variation in the ITS regions appeared to be falsely suppressed
      DADA2用于长读长时，ITS区域的变化会收到抑制

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      • A
        anneng 最后由 编辑

        为什么要去噪？
        https://forum.qiime2.org/t/metaphlan2-vs-vsearch-for-fungal-metagenomic-shotgun-sequences/6536
        Dereplication and clustering make sense when you have a single region, but it’s not designed to work with data from the full genome.

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        • A
          anneng 最后由 编辑

          A practical guide to amplicon
          and metagenomic analysis of microbiome data

          e1613612-7628-4ca4-b6c8-9389534ee93f-image.png
          b2373005-b158-4060-b634-b3dfa1a4ffc1-image.png

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          • A
            anneng 最后由 编辑

            https://astrobiomike.github.io/misc/amplicon_and_metagen
            Amplicon and metagenomics overview
            fbb18c48-1eee-4126-a62b-b789c9aba9e0-image.png
            667f0bf3-e32f-4ccf-9cf8-4464163fe263-image.png

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            • A
              anneng 最后由 编辑

              https://www.nature.com/articles/ismej2017119
              Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
              7b544a81-7a38-4f16-b697-f393aca1a384-image.png

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              • A
                anneng 最后由 编辑

                https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6427-1
                Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

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                • A
                  anneng 最后由 编辑

                  f1000research-320860.pdf
                  f89613d5-8bb8-4251-ba74-661630562948-image.png

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                  • A
                    anneng 最后由 编辑

                    https://microbiome.netlify.app/index.html
                    Microbiome in R
                    Exploring microbiome analysis using R

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                    • A
                      anneng 最后由 编辑

                      Computational Methods for Microbiome Analysis
                      Computational Methods for Microbiome Analysis.PDF

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                      • A
                        anneng 最后由 编辑

                        https://academic.oup.com/nar/article/48/16/e93/5868338?login=false
                        Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju

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                        • A
                          anneng 最后由 编辑

                          https://www.nature.com/articles/s41597-022-01308-3
                          Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models

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                          • A
                            anneng 最后由 编辑

                            https://assets.researchsquare.com/files/rs-1731798/v1/10f6aaca-0ab4-4ad5-b9e2-fc3489b8f0d1.pdf?c=1655233477
                            Comparison of Oxford Nanopore Technologies and
                            Illumina MiSeq sequencing with mock communities and
                            agricultural soil

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                            • A
                              anneng 最后由 编辑

                              Carlotta-Catozzi-compresso.pdf

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                              • A
                                anneng 最后由 编辑

                                https://peerj.com/articles/5364/
                                Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

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                                • A
                                  anneng 最后由 编辑

                                  https://www.mdpi.com/1422-0067/23/17/9834/htm
                                  Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics
                                  3d091668-c053-4aa3-a2b9-6988c37d1464-image.png

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