Calculate Alpha Diversity out of several Fastq files.

Question

[gapey17315]

I have several fastq files. (file1.fastq, file2.fastq, .... file14.fastq) that consists of the same population. Does anyone know what the most efficient way is to calculate the population diversity (alpha diversity) directly from fastq files?

[antonioggsousa]

Hi,

As far as I know, you can't calculate alpha diversity directly from fastq files. I don't know what you have in each one of these fastq files, but quite often each fastq file corresponds to a biological sample or a biological replicate. In any case, you have sequences from multiple "individuals" (assuming that you've fastq files from microbiota) in the same file. Thus, first you must "decompress" this information into a community/population/OTU/ASV table where you've taxa in the rows and samples in the columns. Only after this step, which involves several sequential steps like QC, dereplication, clustering or denoising and taxonomic classification. The latter is not required for alpha-diversity because you quite often calculate the metric based on OTUs or ASVs rather than at a taxonomic level.

You may check dada2 R package that allows you to process fastq sequences until get a ASV (taxonomic) table. You can use this result to integrate it with phyloseq R package to calculate alpha-diversity. QIIME 2 is a command-line software that integrates multiple standalone tools like dada2 that you may want to have a look into.

I hope this helps,

António

[gapey17315]

Thank you, your answer helped. I have used phyloseq so far with no problems.