微生物的文献整理
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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. -
A practical guide to amplicon
and metagenomic analysis of microbiome data
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https://astrobiomike.github.io/misc/amplicon_and_metagen
Amplicon and metagenomics overview
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https://www.nature.com/articles/ismej2017119
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
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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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https://microbiome.netlify.app/index.html
Microbiome in R
Exploring microbiome analysis using R -
Computational Methods for Microbiome Analysis
Computational Methods for Microbiome Analysis.PDF -
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 -
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 -
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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https://peerj.com/articles/5364/
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches -
https://www.mdpi.com/1422-0067/23/17/9834/htm
Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics
