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The assembly workflow

PacBio de novo assembly

step1: filter the raw reads using SMRTAnalysis

step2: run Falcon and PBcR assembly respectively Falcon: fc_run.py ./fc_run.cfg PBcR assembly: PBcR -maxCoverage 40 -l alpina -s pacbio.spec -pbCNS -fastq Aalpina.filtered_subreads.fastq genomeSize=375000000 localStaging=/scratch

step3: polish the assemblies using Quiver with the filtered reads

step4: map illumina reads to the assemblies and do further correction

Optical map de novo assembly

Misassembly-corrected hybrid assembly by optical consensus maps(CMAPs)

Step1: align CMAPs to sequence assemblies with stringent and loose initial alignment p-value, respectively

Step2: find conflicting alignments

Step3: