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PacBio data assembly with Celera

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
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updated by Ram Ram • written by mhasa006 mhasa006

3 answers

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.

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updated by Ram Ram • written by rhall rhall

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)

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updated by Ram Ram • written by thackl thackl

If you are assembling a small genome, and if your PacBio reads are corrected reads, then SPAdes or MIRA should do a good job.

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updated by Ram Ram • written by h.mon h.mon

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?

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written by mhasa006 mhasa006

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

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updated by Ram Ram • written by Rohit Rohit

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