MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Table 1 Capabilities of MetaPop compared to existing complementary bioinformatic pipelines

	MetaPop	Anvi’o	MIDAS	metaSNV	InStrain
Input files:
QC’d reads	No	No	Yes	No	No
BAM file(s)	Yes	Yes	No	Yes	Yes
Genome fasta file	Yes	Yes	No	Yes	Yes
Gene file	No	No	No	Yes	Yes
Read/bp numbers	Yes	No	No	No	No
Preprocessing:
Sorts & indexes BAM files	Yes	Yes	Yes	No	No
Removes spuriously mapped reads from each genome	Yes	No	Yes	No	Yes
Removes genomes with low horizontal coverage in each BAM	Yes	Yes	Yes	Yes	Yes
Identifies genomes with high read depth coverage per BAM	Yes	Yes	Yes	Yes	Yes
Performs gene calls	Yes	Yes	Yes	No	No
Macrodiversity:
Calculates raw population abundances	Yes	Yes	Yes	Yes	No
Normalizes population abundances across samples	Yes	No	No	No	No
Calculates alpha-diversity	Yes	No	No	No	No
Calculates beta-diversity	Yes	No	No	No	No
Microdiversity:
Calls SNVs	Yes	Yes	Yes	Yes	Yes
Does consensus SNP calling	Yes	No	No	No	Yes
Identifies codon variants	Yes	Yes	No	No	No
Downsamples data prior to population genetics calculations	Yes	No	Yes	No	No
Calculates intra-population diversity	Yes	Yes	Yes	Yes	Yes
Calculates inter-population diversity	Yes	No	No	Yes	Yes
Calculates linkage disequilibrium	No	No	No	No	Yes
Additional analyses:
Contig annotation	No	Yes	Yes	No	No
Codon bias analyses	Yes	No (but does calculate codon usage)	No	No	No
Dereplicates genomes	No	Yes	No	No	No
Contig binning	No	Yes	No	No	No
Pangenome analyses	No	Yes	Yes	No	No
Outputs:
Text data files	Yes	Yes	Yes	Yes	Yes
Visualizations	Yes	Yes	No	No	Yes

ISSN: 2049-2618