Table 1:

Collection of tools available for sequencing data analysis in WBE and SARS-CoV-2 lineage proportion estimation. We distinguish the tools roughly based on their approach to define a reference set into those using predefined marker mutations and those relying on full genome sequences or both. The 2 implementations we selected for reference construction and our comparison are indicated in bold. Please note that C-WAP [31] wraps multiple approaches while also including a new mutation-based tool, LINDEC.

Mutation based
Tool	Citation	Code
MAMUSS	[20]	github.com/lifehashopes/MAMUSS
Freyja	[21]	github.com/andersen-lab/Freyja
Lineagespot	[22]	github.com/nikopech/lineagespot
LCS	[23]	github.com/rvalieris/LCS
Alcov	[24]	github.com/Ellmen/alcov
VaQuERo	[16]	github.com/fabou-uobaf/VaQuERo
MMMVI	[25]	github.com/dorbarker/voc-identify
PiGx	[26]	github.com/BIMSBbioinfo/pigx_sars-cov-2
SAMRefiner	[18]	github.com/degregory/SAM_Refiner
COJAC	[10]	github.com/cbg-ethz/cojac
wastewaterSPAdes	[30]	—
gromstole	—	github.com/PoonLab/gromstole
CovMix	—	github.com/chrisquince/covmix

Sequence Based
Tool	Citation	Code
VLQ-nf	this study	https://github.com/rki-mf1/VLQ-nf
VLQ	[29]	github.com/baymlab/wastewater_analysis
VirPool	[27]	github.com/fmfi-compbio/virpool
V-pipe SC2	[28]	cbg-ethz.github.io/V-pipe/sars-cov-2

Mutation Based And Sequence Based
Tool	Citation	Code
C-WAP	[31]	github.com/CFSAN-Biostatistics/C-WAP