Raw PacBio reads (CCS) were error corrected using FALCON and assembled using canu. The settings used were as follows:
Settings used for error-correction were as follows:
#### Input options
[General]
input_fofn=input.fofn
input_type=raw
pa_DBdust_option=
pa_fasta_filter_option=streamed-median
target=pre-assembly
skip_checks=False
LA4Falcon_preload=false
#### Data Partitioning
pa_DBsplit_option= -x500 -s400
ovlp_DBsplit_option= -x500 -s400
#### Repeat Masking
pa_HPCTANmask_option=
#no-op repmask param set
pa_REPmask_code=0,300;0,300;0,300
####Pre-assembly
# adjust to your genome size
genome_size = 2400000000
seed_coverage = 45 #adjusted according to datasets
length_cutoff = -1
pa_HPCdaligner_option= -k14 -e0.75 -s100 -l3000 -h240 -w8 -H10310
pa_daligner_option= -k18 -e0.80 -l1000 -h256 -w8 -s100
falcon_sense_option= --min_idt 0.70 --min_cov 2 --max_n_read 200
falcon_sense_greedy=False
canu assembler was run on the corrected reads as follows:
canu -assemble \
-p ${FILE} \
-d ${FILE}-out \
genomeSize=2.4g \
-pacbio-corrected ${FILE}.corrected.fasta \
useGrid=true \
minReadLength=15000 \
minOverlapLength=3000 \
correctedErrorRate=0.065 \
corMhapSensitivity=normal \
ovlMerThreshold=500 \
utgOvlMerThreshold=200 \
cnsMemory=12 \
cnsThreads=12 \
merylThreads=24 \
batThreads=24 \
gfaThreads=24 \
BioNano Solve was run as suggested by BioNano documentation.