PacBio data assembly with Celera

Question

[mhasa006]

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?

Answer 1

[rhall]

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

Answer 2

[thackl]

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)

Answer 3

[h.mon]

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

[mhasa006]

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?

[Rohit]

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