Table 7.

A list of software and parameters used for genome analysis.

Softwares	Version	Parameters/Commands
FLASH	1.2.11	default
JELLYFISH	2.2.6	-C -m 17
Platanus trim	1.0.7	platanus_trim (for PE reads), platanus_internal_trim (for MP reads)
Platanus	1.2.4	step-1: assemble -m 2048, step-2: scaffold, step-3: gap_close
SSPACE Standard	3.0	default
DIAMOND	0.9.24	default
MEGAN	6.15.2	default
QUAST	4.5	default
BUSCO	3.0.2	-l arthropoda_odb9
RepeatMasker	4.0.7	-e ncbi -pa 4
RepeatModeler	1.0.10	-engine ncbi -pa 4
LSC	2.0	default
GMAP	2018-07-04	-B 5
derive-gene-models-from-PacBio.pl		default
TransDecoder	3.0.1	step-1: TransDecoder.LongOrfs, step-2: TransDecoder.Predict
Tophat	2.1.1	–microexon-search–mate-std-dev 26–mate-inner-dist 38–min-intron-length 30–min-coverage-intron 30–min-segment-intron 30
GenBlastA	1.0.4	-p T -e 1e-5 -g T -f F -a 0.5 -d 100000 -r 100 -c 0.01 -s -100
Exonerate	2.2.0	–model protein2genome –percent 30 –showvulgar no –showalignment yes–showquerygff no –showtargetgff yes –targetchunkid 1–targetchunktotal 100
BRAKER	2.0	–species = T. longiramus – AUGUSTUS_CONFIG_PATH = augustus/config – AUGUSTUS_BIN_PATH = augustus/bin – AUGUSTUS_SCRIPTS_PATH = augustus/scripts – GENEMARK_PATH = gm_et/gmes_petap – bam = tophat/accepted_hits.bam–prot_seq = PacBio-derived.gene-models.transdecoder.pep.fasta –alternatives-from-evidence = true –prg = exonerate
InterProscan	5.16–55.0	-appl HAMAP,ProDom,PRINTS,Pfam,TIGRFAM,SUPERFAMILY,ProSitePatterns,ProSiteProfiles -goterms -iprlookup
OrthoMCL	2.0.9	-I 1.5
MUSCLE	3.8.31	default
ETE	3.1.1	trimal -gappyout
RAxML	8.2.10	-m PROTGAMMAJTT
MEGA	7.00	megacc
CAFE	4.0	default