Taxonomic assignment of bins found by Maxbin2

Question

[Hansen_869]

Hi there!

I have been running Maxbin2 to generate bins from metagenomic data files (bacteria). The output is a series of bins (in fasta), but with no taxonomic assignment. I need a tool to annotate these bins, into to their respective organism names. I am running my tools in Snakemake, and thus need a command-line tool.

So far, I've been looking at MEGAN, metabin and cat/bat. MEGAN only has a graphic interface. Metabin is impossible to find data on how to use. Cat/bat requires me to download the entire database of taxonomy files, which is too huge for my PC.

Ideally, I need a tool that annotates the bins, is command-line based and doesn't require me to download huge files, but rather use an online database.

Thanks!

[gb]

Would metaphlan2 be an option?

http://huttenhower.sph.harvard.edu/metaphlan2

[Hansen_869]

Thanks for your answer, however I fail to see where it says metaphlan2 can be used with bins. Looks like it is only for a collecting of reads?

Answer 1

[Mensur Dlakic]

Ideally, I need a tool that annotates the bins, is command-line based and doesn't require me to download huge files, but rather use an online database.

Not sure that such a tool exists. These days most people have no problem with disk space or downloading large files, so developers have little incentive to make tools that work directly with large online databases. Not to mention that those large databases prefer less online traffic if possible.

While CheckM does not fit your criteria - there is a large database to download - it may be worth your time. It will assess completeness and contamination of your bins, as well as perform taxonomic assignments.

[Hansen_869]

Hi Mensur,

CheckM seems to do the job, and the database is not too big. However, when I run checkM, i get the taxonomic assignments in my terminal, but i fail to see a file containing the information regarding that. I'm using the default Lineage-specific workflow that they suggest.

[jubillante]

This is a late reply but for anyone wondering how to fix this use the option -f to redirect the stdout (with taxonomy table and stats) to a file:

  checkm lineage_wf bins outputfolder -f output.txt