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?
Question: PacBio data assembly with Celera
0
mhasa006 • 50 wrote:
3
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.
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/De-Novo-Assembly
http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
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thackl • 2.8k 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)
1
h.mon ♦ 32k 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.
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