Frequently Asked Questions

Q: Do I need to install mamba?

A: Installing mamba is optional. Simply using conda should be enough, although considerably slower, to create environments. If using only conda you may need to add the argument --conda-frontend conda when executing snakemake.

Q: Can I use FooDMe for single end reads?

A: FooDMe is designed for Illumina paired-end sequencing and single read sequencing is not supported.

Q: Are IonTorrent data supported?

A: Not yet. But it should be possible with some modifications. Get in touch if this is something you need.

Q: Can I use FooDMe for bacteria metabarcoding?

A: You could but it is not recommended. There are pipeline more suitables for micro-organisms out there.

Q: Can I use nucleotide databases other than RefSeq or BLAST NT (e.g. BOLD)?

A: Any nucleotide database can be used, however they need to be formatted by the BLAST+ tools suit to be usable in FooDMe. Consult the BLAST documentation for instructions.

Q: In the reports, some decimals are point-separated and others are comma-separated. Why is that and how do I fix it?

A: The comma-spearated values are generated in some cases depending on your system's langugae (e.g. French, German,...). To enforce point-separated values, change your system locale by modifying the ~/.bashrc file with LANG=C.