NGS WGS analysis .fna file

Question

[ahmer]

Hello, I have done WGS of my bacterial strains and got some preprocessed Illumina sequencing files in .fna format. It has a format like this

>1 length=400016 depth=0.86x
the sequence
>2 length=323455 depth=1.00x

and so on to >102 I want to know how to deal with this .fna file.

Best regards,

Thanks

[cpad0112]

it is really difficult to put information in the context, based on your query with minimal information. Since you have only sequences with depth in header, talk to your PI or friends, to decide upon depth that is signficiant for your experimental condition. Filter by depth (but that would be messy given the format you have) and blast the sequences against prokaryote genomic (NCBI blast) and proteomic resources (Rapsearch, Diamond), You would get representative bacterial strains/species/Genus in your data. If you are not sure how to proceed, ask the same person/core facility, who gave you this file, for downstream analysis (for eg species/strain identification, alpha diversity, beta diversity etc).

If you have more time and have bioinformatics sources around, request for WGS raw data (as .fastq ) and go for metagenomics pipelines. This would give you better understanding of experimental output and you can control analysis parameters for meaningful output.