#28 use Celera Assembler with corrected PacBio reads

[medhat]

Can we use Celera Assembler with precorrected pacbio reads :
runCA -d directory -p prefix corrected_pacBio.fasta

[Sergey Koren]

Yes, you’d have to first convert it to a frg format using fastqToCA. However, I’d suggest using Canu instead.

On Apr 15, 2016, at 8:44 AM, medhat hmedhat@users.sf.net wrote:

[support-requests:#28] https://sourceforge.net/p/wgs-assembler/support-requests/28/ use Celera Assembler with corrected PacBio reads

Status: open
Group: v1.0_(example)
Created: Fri Apr 15, 2016 12:44 PM UTC by medhat
Last Updated: Fri Apr 15, 2016 12:44 PM UTC
Owner: nobody

Can we use Celera Assembler with precorrected pacbio reads :
runCA -d directory -p prefix corrected_pacBio.fasta

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[medhat]

fastqToCA -l PacBio -s corrected_pacBio_seq.fasta > new.frg

There is no need to -q "Fasta file of quality values" cause I do not have it.

[Sergey Koren]

FastqToCA requires fastq input not fasta so you’ll have to add quality values so you’ll have to generate uniform qualities for all reads. You also need to specify the read type option, run the command to see the list of options it supports.

On Apr 16, 2016, at 4:39 AM, medhat hmedhat@users.sf.net wrote:

fastqToCA -l PacBio -s corrected_pacBio_seq.fasta > new.frg

There is no need to -q "Fasta file of quality values" cause I do not have it.

[support-requests:#28] https://sourceforge.net/p/wgs-assembler/support-requests/28/ use Celera Assembler with corrected PacBio reads

Status: open
Group: v1.0_(example)
Created: Fri Apr 15, 2016 12:44 PM UTC by medhat
Last Updated: Fri Apr 15, 2016 12:44 PM UTC
Owner: nobody

Can we use Celera Assembler with precorrected pacbio reads :
runCA -d directory -p prefix corrected_pacBio.fasta

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/wgs-assembler/support-requests/28/ https://sourceforge.net/p/wgs-assembler/support-requests/28/
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[medhat]

Thanks a lot for answering,
According to what you said;

First I need to do:

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

to have my corrected pacbio reads in fastq from fasta

second I need to use fastqToCA :

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

Thanks for help