nanoporetech/ont-assembly-polish

time saving

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wzylin commented

HI,
If I already used Canu to do the assembly.
How can I use this pipeline to do the rest of the jobs?
For saving time, I dont wanna assemble it again.
Thanks.

bsipos commented

Hi wzylin,

To start with an existing assembly do the following:

  1. Edit config.mk as usual
  2. issue "make wdir" to create working directory
  3. Place the assembly under <working_directory>/canu-assembly/canu.contigs.fasta
  4. Comment out most lines for the canu assembly target in analysis.mk
    canu_assembly: $(CANU_CONTIGS) $(WDT)
    $(CANU_CONTIGS): $(NANOPORE_READS)
    @echo Assembling nanopore reads using canu.
    @canu
    # -p $(CANU_PREFIX)
    # -d $(CANU_DIR)
    # genomeSize=$(CANU_GENOME_SIZE)
    # -nanopore-raw $(NANOPORE_READS) $(CANU_PARAMETERS)
  5. issue "make all" to perform correction with racon and pilon

Hope this helps, please write a message if you run into any problems.

Botond