Racon assembly output with circlator

[mictadlo]

Hi, I ran a PacBio chloroplast assembly with Racon in the following way:

source activate minimap2
minimap2 -t 8 -x ava-pb \
    input.fasta \
    input.fasta | gzip -1 > output.paf.gz

source activate miniasm
miniasm -Rc2 -f \
    input.fasta \
    output.paf.gz > output.gfa

awk '/^S/{print ">"$2"\n"$3}' output.gfa | fold >  output.gfa.fasta

# Correction 1
source activate minimap2
minimap2 -t 8 -ax map-pb \
    output.gfa.fasta \
    input.fasta > output.gfa1.sam

source activate racon
racon -t 8 \
    input.fasta \
    output.gfa1.sam \
    output.gfa.fasta > output.racon1.fasta

# Correction 2
source activate minimap2
minimap2 -t 8 -ax map-pb \
    output.racon1.fasta \
    input.fasta > output.gfa2.sam

source activate racon
racon -t 8 \
    input.fasta \
    output.gfa2.sam \
    output.racon1.fasta > output.racon2.fasta

How can I get the required corrected PacBio reads for circlator all assembly.fasta reads output_directory?

Thank you in advance.

Michal

[kassammo]

Hello Michal

Did you find a way to use circlator with Racon assembly output.

Thank you in advance,

Mohamed

[mictadlo]

Hi Mohamed, I add the above pipeline into the original code but I ran into a problem. The code can be found as PR here.

Michal