Genome assembly Using Celera Assembler with corrected data from LoRDEC

[Medhat]

Hi,
I corrected PacBio reads Using LoRDEC tool , now I have a corrected fasta file.
My question,
Can I use Celera Assembler with the corrected reads from LoRDEC to do assembly?

[rhall]

Yes, you should be able to treat them like any other accurate long read, i.e. sanger. What coverage do you have, raw pacbio, corrected pacbio. You will need ~15x corrected pacbio. If you have >35x raw pacbio I would also try going straight into canu https://github.com/marbl/canu

[Medhat]

Unfortunately the raw read coverage is low ~1x , so I can not go for canu.

To run celera assembler

runCA -d directory -p prefix myPacBio.frg

How to create myPacBio.frg from corrected pacbio read that are fasta file no quality ;

so do I need first to run something like this !!

java -jar convertFastaAndQualToFastq.jar corrected_pacbio.fasta > corrected_pacbio.fastq

then use fastqToCA like this:

fastqToCA -libraryname MycorrectedPacBIo -technology pacbio-corrected -reads corrected_pacbio.fastq > ca.frg

Or there is another solution

Thanks a lot for help.

[rhall]

It isn't possible to assemble 1x of data no matter what the error. Given the statistics of coverage much of the genome will not be sampled, i.e. 0 coverage.
Even gap filling an existing assembly will require at least 5x, preferably closer to 15x. https://github.com/PacificBioscience...Bio-Long-Reads