canu的使用

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curl -L -o pacbio.fastq http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p6_25x.filtered.fastq
curl -L -o oxford.fasta http://nanopore.s3.climb.ac.uk/MAP006-PCR-1_2D_pass.fasta

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canu \
 -p ecoli -d ecoli-pacbio \
 genomeSize=4.8m \
 -pacbio-raw pacbio.fastq

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canu -correct \
  -p ecoli -d ecoli \
  genomeSize=4.8m \
  -pacbio-raw  pacbio.fastq

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canu -trim \
  -p ecoli -d ecoli \
  genomeSize=4.8m \
  -pacbio-corrected ecoli/ecoli.correctedReads.fasta.gz

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canu -assemble \
  -p ecoli -d ecoli-erate-0.039 \
  genomeSize=4.8m \
  correctedErrorRate=0.039 \
  -pacbio-corrected ecoli/ecoli.trimmedReads.fasta.gz

canu -assemble \
  -p ecoli -d ecoli-erate-0.075 \
  genomeSize=4.8m \
  correctedErrorRate=0.075 \
  -pacbio-corrected ecoli/ecoli.trimmedReads.fasta.gz

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useGrid=false \

gnuplotImageFormat=canvas \ or
gnuplotTested=true ##跳过gnuplot检测，在运行过程中不再使用gnuplot生成图片

## 如不添加上方gnuplot参数，则容易在程序启动前自检中出现如下报错
##（此问题似乎在1.7.1版本修复）
##ERROR:  Failed to detect a suitable output format for gnuplot.
##ERROR:  Looked for png, svg and gif, found none of them.

## java SE 8