Bins and functional annotation

Question

[h.l.wong]

Hi all,

I have a couple of questions to ask.

1. I have assembled sequences from a microbial community and have used Prodigal to produce .gff and .fasta files with it. Now I have no idea what to do with those files for downstream analysis and functional annotation. Any suggestions are welcome.

2. I have received ~500 bins in .fasta format. Should I blast them to see what microbes they are or are there any other methods to analyse them?

Cheers and many thanks

Alan

Answer 1

[Asaf]

You can use HumanN2 software to predict metabolic pathways. You can also try BLASTkoala of KEGG.

Answer 2

[robert.kwapich]

If you are working with microbiome: Check microbiome helper, and metagenomic SOP.

https://github.com/mlangill/microbiome_helper/wiki/Metagenomic-standard-operating-procedure