#pacbio corrected reads
#obtained via: Canu
Canu snapshot v1.6 +120 changes (r8532 6ed280b7565194370584994956987ea4dae10a05)

canu -correct -p 2410-e -d 2410-e-correct genomeSize=2.75g useGrid=true gridEngine=slurm gridOptionsJobName=24e-all maxThreads=24 minMemory=64g maxMemory=256g gridOptions="-t 144:00:00 --mem 256G" minThreads=8 saveReads=true -pacbio-raw 2410-e.all.subreads.bam.fastq

#mapping against mm10
#obtained via: ngmlr
ngmlr -t 20 -r mm10.fasta -q 2410-e-default.correctedReads.fasta -o mm10.fasta.2410-e-default.correctedReads.fasta.sam

#vcf
#obtained via: Sniffles

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minimap2 -ax map-hifi mm10.fasta SRR11606870_subreads.fastq.gz > SRR11606870_subreads.mm10.sam
samtools view -b SRR11606870_subreads.mm10.sam > SRR11606870_subreads.mm10.bam
samtools sort SRR11606870_subreads.mm10.bam > SRR11606870_subreads.mm10.sorted.bam
samtools index SRR11606870_subreads.mm10.sorted.bam