Table 1.

Comparison of nf-core/mag’s functionality with commonly used metagenome assembly and binning pipelines. A more detailed comparison is shown in Supplementary Table S1

	Functionality	Muffin v1.0.3	ATLAS v2.6a2	nf-core/mag v2.1.0
Assembly	Hybrid assembly	Yes	Partial	Yes
	Reassembly after binning	Yes	No	No
	Group-wise co-assembly	No	No	Yes
Genome binning	Group-wise co-abundances used for binning	No	Yes	Yes
	Bin refinement	Yes	Yes	No
	MAG abundance estimation	No	Yes	Yes
Annotation	Taxonomic classification	Yes	Yes	Yes
	Functional annotation	Yes	Yes	No
Usability	Reproducibility	No	No	Yes
	Adherence to set of strict best-practice guidelines for pipeline development	No	No	Yes