Software Parameters and Database

Analysis Content	Software Name	Version	Main parameters
Raw Data Quality Control	fastp	0.21.0	fastp -q 10 -u 50 -y -g -Y 10 -e 20 -l 100 -b 150 -B 150
Genome Alignment	bwa-mem2	2.2	bwa-mem2 mem -t 4 -M
Alignments Sort	samtools	1.9	samtools sort
Genome de-redundancy	samtools	1.9	samtools rmdup
Sequencing Depth Statistics	mosdepth	0.3.1	-t 4 --flag 0 -x
Comparison Efficiency Statistics	samtools	1.9	samtools flagstat
Insert Fragment Statistics	picard	1.94	CollectInsertSizeMetrics.jar VALIDATION_STRINGENCY=LENIENT
Variation Detection	GATK	3.8	-XX:ParallelGCThreads=5 -Xmx20G -jar GenomeAnalysisTK.jar -T HaplotypeCaller --indelSizeToEliminateInRefModel 50 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000
Variation Annotation	SnpEff	3.6c	default
SV Detection	Manta	1.6.0	default
CNV Detection	FREEC	11.0	-conf
Circos Graph Drawing	circos	2.0	default
Alignment Software in Functional Annotation	diamond	2.0.15	-k 100 -e -evalue 1e-5 -f 5

Database	Description	Homepage
NR	non-redundant protein sequence database	ftp://ftp.ncbi.nih.gov/blast/db/
Swiss-Prot	A manually annotated, non-redundant protein sequence database	http://www.uniprot.org/
GO	Gene Ontology database	http://www.geneontology.org/
COG	The database of Clusters of Orthologous Groups of proteins	http://www.ncbi.nlm.nih.gov/COG/
KOG	The database of Clusters of Protein homology	http://www.ncbi.nlm.nih.gov/KOG/
Pfam	The database of Homologous protein family	http://pfam.xfam.org/
KEGG	The database of Kyoto Encyclopedia of Genes and Genomes	http://www.genome.jp/kegg/
eggNOG	A database of orthology relationships, functional annotation, and gene evolutionary histories	http://eggnog5.embl.de/#/app/home
TrEMBL	Unreviewed annotated, redundant protein sequence database	http://www.uniprot.org/