Question: PacBio data assembly with Celera
0
gravatar for mhasa006
4.0 years ago by
mhasa00650
United States
mhasa00650 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 • 2.1k views
ADD COMMENTlink modified 4.0 years ago by thackl2.6k • written 4.0 years ago by mhasa00650
3
gravatar for rhall
4.0 years ago by
rhall160
United States
rhall160 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 COMMENTlink written 4.0 years ago by rhall160
3
gravatar for thackl
4.0 years ago by
thackl2.6k
MIT
thackl2.6k 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 COMMENTlink modified 4.0 years ago • written 4.0 years ago by thackl2.6k
1
gravatar for h.mon
4.0 years ago by
h.mon25k
Brazil
h.mon25k 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 COMMENTlink written 4.0 years ago by h.mon25k

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 REPLYlink written 4.0 years ago by mhasa00650

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

ADD REPLYlink written 3.9 years ago by Rohit1.3k
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