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Nanopore metagenomics analysis

I have tones of FAST5 files from MiniON (obtained from intestines of ticks) and my goal is to analyse the species composition (microbiome analysis). We used 16S barcoding kit for Min106 flowcell. Can anyone help me to understand what tools to use step by step to perform it except EPI2ME.

ont metagenomics microbiome
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updated by Chris Dean • Chris Dean • written by kirillkirilenko • kirillkirilenko

There are many ways to accomplish this goal; however, it will depend on the type of data you generated. Sometimes people use the term metagenomics to mean different things, e.g., targeted sequencing of an amplicon or untargeted sequencing of all genetic content. Can you edit your question to clarify the type of data you have (e.g., 16S/18S or shotgun metagenomic data)?

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written by Chris Dean • Chris Dean

2 answers

A popular choice for the processing and analysis of 16S marker genes is the DADA2 pipeline. The program is implemented in R, has great documentation and tutorials, and is regularly updated. Although many of the tutorials focus on short-read data, there are examples of the program being extended for longer reads (e.g., DADA2 + PacBio: Fecal Samples).

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written by Chris Dean • Chris Dean

To get a first pass look at your data you can try this webtool easily: https://www.bioinformatics.uni-muenster.de/tools/metag/usage/index.hbi?lang=en

However, to properly analyse 16S requires skill. I have seen some great discussions on the nanopore community site about this.

I'm not a great fan of 16S, actually, I believe it's ripe for the dustbin, so I'll leave it at that.

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written by colindaven colindaven

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