PacBio data assembly with Celera

Question: PacBio data assembly with Celera

4.4 years ago by

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 • 2.3k views

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modified 4.4 years ago by thackl • 2.7k • written 4.4 years ago by mhasa006 • 50

4.4 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 4.4 years ago by rhall • 160

4.4 years ago by

thackl • 2.7k

MIT

thackl • 2.7k 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 4.4 years ago • written 4.4 years ago by thackl • 2.7k

4.4 years ago by

h.mon ♦ 28k

Brazil

h.mon ♦ 28k 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 4.4 years ago by h.mon ♦ 28k

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 4.4 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 4.3 years ago by Rohit • 1.4k

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