AV454 how to assemble HIV envelope fastq reads?

[Peter Pham]

Hi All,

We're trying to use AV454 to assemble HIV envelope reads in fastq format.


From the online forum, I find out the following commands to execute AV454:

AssembleViral454 ORG=smallgenome GSIZE=30000 PRE=full_path_name_to_your_pre DATA=smallgenome_assembly RUN=2013.07.10.run REFERENCE=full_path_name_to_smallgenome_ref

AssembleViral454 ORG='HIV' GSIZE='3000' PRE=PRE/ DATA=DATA/ RUN=RUN SFF_DIR=SFF REFERENCE='murray_ref_seq'


I also read the http://www.broadinstitute.org/crd/wiki/index.php/Input.
However, I don't know how to setup the DATA directory if I just have the fastq input file.

Could you give me a hint or point me the some sources how to run AV454 with the fastq input file?

Thanks a lot,

Peter