Racon instead Sparc

[mictadlo]

Hi, Did anyone run racon on DBG2OLC output instead of Sparc?

Thank you in advance,

Michal

[rvaser]

Hi Michal, we did a comparison between Sparc and Racon in our paper (https://doi.org/10.1101/gr.214270.116), although that was with miniasm raw assembly. Haven't tried it on DBG2OLC output.

Best regards, Robert

[mictadlo]

Do you think these commands are correct to run racon?

DBG2OLC KmerCovTh 2 AdaptiveTh 0.01 MinOverlap 20 RemoveChimera 1 Contigs Contigs-1000.txt k 17 f input.fasta

cat Contigs-1000.txt input.fasta > ctg_pb.fasta

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

source activate racon 
racon -t 8 \ 
    ctg_pb.fasta \ 
    output.gfa1.sam \ 
    backbone_raw.fasta > output.racon1.fasta 

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

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

Thank you in advance,

Michal

[rvaser]

Hi Michal, what is stored in input.fasta and what in backbone_raw.fasta?

Best regards, Robert

[mictadlo]

Hi Robert,

• input.fasta contains the raw PacBio reads.
• backbone_raw.fasta is DBG2OLC output.
• Contigs-1000.txt is the Illumina assembly.

Thank you in advance.

Michal

[rvaser]

Hi Michal, the commands look fine but I am not sure what the goal is by using Illumina assembly in polishing. If the assembly obtained from DBG2OLC is not polished, you can run two iterations of racon with PB reads and one iteration with Illumina reads (not Illumina contigs, as they will have much lesser coverage). If the DBG2OLC assembly was polished with Sparc, you can run one iteration of racon with Illumina reads.

Best regards, Robert

[mictadlo]

Hi Robert, I combined them because of this https://github.com/yechengxi/DBG2OLC#step-3-call-consensus . I would like to run only racon. Do I have to include only the PacBio reads?

Thank you in advance,

Michal

[rvaser]

Hi Michal, if you have done everything up to step 3 of the DBG2OLC pipeline, use only the PB reads to polish the backbone. Optionally, you can polish with Illumina afterwards.

Best regards, Robert

[mictadlo]

Hi Robert, Do you think the command for minimap and racon are correct?

DBG2OLC KmerCovTh 2 AdaptiveTh 0.01 MinOverlap 20 RemoveChimera 1 Contigs sparse_pregraph.contig-1000.fasta k 17 f contamination_unmapped-5k.fasta

# Correction 1
source activate minimap2
minimap2 -t 8 -ax map-pb \
    backbone_raw.fasta \
    contamination_unmapped-5k.fasta > output.gfa1.sam

source activate racon
racon -t 8 \
    contamination_unmapped-5k.fasta \
    output.gfa1.sam \
    backbone_raw.fasta > output.racon1.fasta

# Correction 2
source activate minimap2
minimap2 -t 8 -ax map-pb \
    output.racon1.fasta \
    contamination_unmapped-5k.fasta > output.gfa2.sam

source activate racon
racon -t 8 \
    contamination_unmapped-5k.fasta \
    output.gfa2.sam \
    output.racon1.fasta > output.racon2.fasta

Thank you in advance,

Best wishes,

Michal

[rvaser]

Hi Michal,

they look fine.

Best regards, Robert

[mictadlo]

Thank you.

[mictadlo]

What is the minimum PacBio reads coverage to run Racon?

Thank you in advance.

Michal

[rvaser]

You can use any coverage, but to get something polished then 3 is the minimum.