Last updated: June 16, 2021

Dependencies for:

1) 00_preprocessing.smk

	- bbmap (suite) (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/)
	- minimap2 (https://github.com/lh3/minimap2)
	- mmseqs2 (https://github.com/soedinglab/MMseqs2)
	- seqkit (https://bioinf.shenwei.me/seqkit/)
	- csvtk (https://github.com/shenwei356/csvtk)
	- samtools (http://www.htslib.org)
	- megahit (https://github.com/voutcn/megahit)
	- flye (https://github.com/fenderglass/Flye)
	- R
		- tidyverse (https://www.tidyverse.org)

2) 01_taxonomic_assignment.smk

	- mmseqs2 (https://github.com/soedinglab/MMseqs2)
	- samtools (http://www.htslib.org)
	- seqkit (https://bioinf.shenwei.me/seqkit/)
	- csvtk (https://github.com/shenwei356/csvtk)
	- taxonkit (https://bioinf.shenwei.me/taxonkit/)
	
