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?
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.
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)