Table 1.

Tools employed in the pipeline, specific versions and settings.

Tool	Purpose	Settings	References	Version	FASTQ	FASTA
fastp	Adapter trimming		[47]	0.20.1	X
BWA mem 2	Alignment	Default	[48]	2.2.1	X
GATK	Variant calling and alignments preprocessing	MQ ≥ 20, BQ ≥ 20, ploidy = 1	[49]	4.2.0.0	X
sambamba	Read deduplication	MQ ≥ 20, BQ ≥ 20, ploidy = 1	[50]	0.8.2	X
samtools	Coverage analysis		[51]	1.12	X
LoFreq	Variant calling	MQ ≥ 20, BQ ≥ 20	[52]	2.1.5	X
BCFtools	Variant calling, normalization and annotation	MQ ≥ 20, BQ ≥ 20	[53]	1.14	X	X
iVar	Variant calling	MQ ≥ 20, BQ ≥ 20	[54]	1.3.1	X
Biopython	Custom variant calling on assemblies sequences based on Needleman-Wunsch global alignment	aligner.mode = ‘global’ aligner.match = 2 aligner.mismatch = −1 aligner.open_gap_score = −3 aligner.extend_gap_score = −0.1 aligner.target_end_gap_score = 0.0 aligner.query_end_gap_score = 0.0	[55]	1.79		X
SnpEff	Functional annotations		[56]	5.0	X	X
VAFator	Technical annotations	MQ > 0, BQ > 0	[14]	1.2.5	X
Pangolin	Lineage calling		[59]	4.1.2	X	X
ConsHMM	Conservation annotations		[57]	Not available	X	X
Pfam	SARS-CoV-2 protein domains		[58]	Not available	X	X