Are There Workflows For Fungal Internal Transcribed Spacer (Its) Analysis?
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9.3 years ago
polangxin ▴ 80

454 sequencing, fungi, nuclear ribosomal internal transcribed spacer(ITS).

are there workflows like mothor/qiime, for analysis ITS?

Thanks!

workflow • 3.7k views
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9.3 years ago
Josh Herr 5.7k

I'm not exactly sure what you mean by a workflow for ITS, but this is what I do for my research so I can explain. There is no specific "Fungal ITS workflow" but if you are going to identify fungal ITS amplicons from environmental samples then you can just use one of many pipelines developed for the analysis of other similar gene regions: QIIME and MOTHUR are probably the two most accepted pipelines for amplicon data from the rRNA operon (16S, 18S, etc.). You'll have to set the parameters of your pipeline in accordance with the type of sequencing data you have and the overall diversity of your sampling environment (soil, plant, human, etc.)...

When you use these pipelines you'll want to use the ITS reference sequence database that was recently constructed for the identification of ITS amplicons. This database comes from a curated set of sequences from numerous sources (UNITE, Lee Taylor's Lab resource, and NCBI/EMBL). Later, this database was appropriated by CLOVR, so you can use it there too.

This paper is in press, but it will give you an overview of what you will do to analyze ITS sequences. Feel free to email me if you have any questions.

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Thanks! it is very helpful!

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