# Additional file 4

# This supplementary file includes the parameters and data used for Zinfandel genome assembly, annotation, variant calling, and validation methods

########
# Data #
########

ESTs
•	Vitis ESTs (NCBI)
•	Vitis vinifera cDNA cDNA Full Length (NCBI)

Iso-Seq
•	Minio et al. 2019
•	Cv. Cabernet Sauvignon (SRP132320)
•	Deseeded whole berries 
•	4 developmental stages: (i) pre-véraison that corresponded to green berries beginning to soften; (ii) véraison that referred to softer berries with 50% red color development; (iii) post-véraison including soft and 100% red-colored berries; and (iv) harvest represented by fully ripe berries equivalent to those used for commercial harvest

Transcriptomes
•	Venturini et al. 2013 - cv. Corvina - pool of 45 tissues
•	Da Silva et al. 2013 - cv. Tannat
•	Unpublished TSA GBXP01 - cv. Cabernet Sauvignon
•	ERX1139708 - Cabernet Sauvignon (http://www.omicsdi.org/dataset/arrayexpress-repository/E-MTAB-3966)


SRA Datasets
•	Blanco-Ulate et al. 2017, PRJNA339456, GEO: GSE85812

•	Cultivar: Zinfandel
•	Deseeded whole berries 
•	Healthy and Red Blotch disease affected plants
•	4 developmental stages: (i) pre-véraison that corresponded to green berries beginning to soften; (ii) véraison that referred to softer berries with 50% red color development; (iii) post-véraison including soft and 100% red-colored berries; and (iv) harvest represented by fully ripe berries equivalent to those used for commercial harvest
•	SRR4043686
•	SRR4043687
•	SRR4043688
•	SRR4043689
•	SRR4043690
•	SRR4043691
•	SRR4043692
•	SRR4043693
•	SRR4043694
•	SRR4043695
•	SRR4043696
•	SRR4043697
•	SRR4043698
•	SRR4043699
•	SRR4043700
•	SRR4043701
•	SRR4043702
•	SRR4043703
•	SRR4043704
•	SRR4043705
•	SRR4043706
•	SRR4043707
•	SRR4043708
•	SRR4043709
•	SRR4043710
•	SRR4043711
•	SRR4043712
•	SRR4043713
•	SRR4043714
•	SRR4043715
•	SRR4043716
•	SRR4043717
•	SRR4043718
•	SRR4043719
•	SRR4043720
•	SRR4043721
•	SRR4043722
•	SRR4043723
•	SRR4043724
•	SRR4043725
•	SRR4043726
•	SRR4043727
•	SRR4043728
•	SRR4043729
•	SRR4043730
•	SRR4043731
•	SRR4043732
•	SRR4043733
•	SRR4043734
•	SRR4043735
•	SRR4043736
•	SRR4043737


Proteins
•	swissProt viridiplantae
•	TAIR10 Arabidopsis
•	Vitis (NCBI)


############
# Settings #
############

Falcon
•	Length cutoff = 13073
•	Length cutoff for pre-assembly = 5000
•	pa_HPCdaligner_option = -k16 -e0.70 -s1000 -t16 -l1000 -h64 -w7 -mtan -mrep2 
•	ovlp_HPCdaligner_option = -k20 -e.96 -s1000 -t32 -l2500 -h256 -mtan -mrep2
•	pa_DBsplit_option = -x500
•	ovlp_DBsplit_option = -x500
•	overlap_filtering_setting = --max_diff 40 --max_cov 45 --min_cov 4


PASA
•	length_cutoff = 13073
•	length_cutoff_pr = 5000
•	pa_HPCdaligner_option = -k16 -e0.70 -s1000 -t16 -l1000 -h64 -w7 -mtan -mrep2
•	ovlp_HPCdaligner_option = -k20 -e.96 -s1000 -t32 -l2500 -h256 -mtan -mrep2
•	pa_DBsplit_option = -x500 
•	ovlp_DBsplit_option = -x500 
•	overlap_filtering_setting = --max_diff 40 --max_cov 45 --min_cov 4


EvidenceModeler
•	ABINITIO_PREDICTION	AUGUSTUS	5
•	ABINITIO_PREDICTION	GeneMark.hmm3	5
•	ABINITIO_PREDICTION	augustus_BUSCOv3	6
•	ABINITIO_PREDICTION	snap	3
•	PROTEIN	protein2genome	1
•	TRANSCRIPT	est2genome	10
•	TRANSCRIPT	PASA_assemblies	20
•	OTHER_PREDICTION	PASA_transdecoder	20 


Trimmomatic, RNA
•	LEADING = 7
•	TRAILING = 7
•	SLIDINGWINDOW = 10:20
•	MINLEN = 36



############################
# Variant Calling Pipeline #
############################

Trimmomatic, DNA
•	Crop = 100
•	Leading = 3
•	Trailing = 3
•	Sliding window = 4:20
•	Min len = 60


##############
# Validation #
##############

MUMMER4
•	nucmer --mum
•	Variant calling
•	•	show-snps (-Clr -x 1)
•	•	show-diff  



Minimap2
•	-ax map-pb 
•	--MD
•	--cs 
•	-L



Clairvoyante
•	--threshold 0.2 
•	--minCoverage 4 
•	--threads 8 
•	--chkpnt_fn Clairvoyante/trainedModels/fullv3-pacbio-ngmlr-hg001+hg002+hg003+hg004-hg19/learningRate1e-3.epoch100.learningRate1e-4.epoch200