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Question: PacBio data assembly with Celera
0
gravatar for mhasa006
5.6 years ago by
mhasa006 • 50
United States
mhasa006 • 50 wrote:

I have a set of PacBio long reads in fastq file. I want to assemble them in contigs. Which assembler will work well? If Celera is the answer, could anyone give me a step by step approach of using celera for assembling PacBio long reads?
pacbio celera assembly • 2.5k views
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modified 5.6 years ago by thackl • 2.8k • written 5.6 years ago by mhasa006 • 50
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gravatar for rhall
5.6 years ago by
rhall • 160
United States
rhall • 160 wrote:

fastq extracted from bax.h5 are not corrected, I would suggest using either HGAP - that is part of PacBio's SMRT Analysis system, or PBcR.

http://www.pacb.com/devnet/

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/De-Novo-Assembly

http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR

 
ADD COMMENT • link written 5.6 years ago by rhall • 160
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gravatar for thackl
5.6 years ago by
thackl • 2.8k
MIT
thackl • 2.8k wrote:

Ideally, if you also have some Illumina data, go for hybrid correction (What tools you use or know for PacBio Long Read error correction?) and assembly with SPAdes (genome <100Mbp)
ADD COMMENT • link modified 5.6 years ago • written 5.6 years ago by thackl • 2.8k
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gravatar for h.mon
5.6 years ago by
h.mon ♦ 32k
Brazil
h.mon ♦ 32k wrote:

If you are assembling a small genome, and if your PacBio reads are corrected reads, then SPAdes or MIRA should do a good job.
ADD COMMENT • link written 5.6 years ago by h.mon ♦ 32k

I don't know if my long reads are corrected. I had a bunch of *.bax.h5 file from which I extracted the .fastq file. Is there way to know if the reads are corrected?

ADD REPLY • link written 5.6 years ago by mhasa006 • 50

I don't think your reads are corrected, since usually error-correction methods produce fastq files 

ADD REPLY • link written 5.5 years ago by Rohit • 1.4k
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