I am a newbie to metagenomics and it is often very confusing on how to analyse my data. I have used the Illumina NextSeq (2 x 150) to sequence a microbial community.
I have used fastQC and trimmomatic for the quality control, and I have assembled the sequences using IDBA-UD. In IDBA-UD, I used command mink=20, maxk=100 for constructing de Bruijn Graph.
There are a lot of output files namely (contig-20.fa, contig-40.fa.....contig-100.fa, contig.fa and scaffold.fa). I would like to do functional annotations and maybe later binning.
Here are the questions:
- Which file(s) should I use? I have the log file showing the statistics but I don't know what criteria should I choose upon.
- What programs do you suggest for functional annotation?
- I intend to use MetaBat for binning, but it needs a BAM file, how can I generate a BAM file?
Thanks for your time on reading my question, if you need anything to be clarified, please let me know.
Cheers and many thanks