search

nanoporetech / ont-assembly-polish

ONT assembly and Illumina polishing pipeline
Mozilla Public License 2.0
91 stars 18 forks source link

time saving #1

Closed wzylin closed 7 years ago

wzylin commented 7 years ago

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 7 years ago

Hi wzylin,

To start with an existing assembly do the following:

1) Edit config.mk as usual 1) issue "make wdir" to create working directory 3) Place the assembly under /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