Hello,
I am new to PacBio data and pipeline. Recently, I got some pacBio data in fastq format instead of bas.h5 format. I tried blasr to run alignment and looks like blasr worked. But I want to try HGAP in SMRT analysis pipeline to do de novo assembly. I read a lot of online posts and did not find how to run HGAP with fastq files. Looks like the SMRT pipeline only support bas.h5 as the input files. Does anyone give me some suggestions how to run de novo assembly with HGAP using the fastq files as input?
Your response would be really appreciated!
Michael
I am new to PacBio data and pipeline. Recently, I got some pacBio data in fastq format instead of bas.h5 format. I tried blasr to run alignment and looks like blasr worked. But I want to try HGAP in SMRT analysis pipeline to do de novo assembly. I read a lot of online posts and did not find how to run HGAP with fastq files. Looks like the SMRT pipeline only support bas.h5 as the input files. Does anyone give me some suggestions how to run de novo assembly with HGAP using the fastq files as input?
Your response would be really appreciated!
Michael
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