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Velvet is a De Bruijn graph assembler works fairly rapidly on short (microbial) genomes. In this tutorial we will use velvet to assemble an E. coli genome from simulated Illumina reads. Genome assembly is quite difficult (though as Oxford Nanopore comes online it will likely get much easier and involve new tools). Genome assembly should only be used when you can not find a reference genome that is close to your own, if you are engaged in metagenomic projects where you don't know what organisms may be present, and in situations where you believe you may have novel sequence insertions into a genome of interest (Note that in this case however you would actually want to grab reads that do not map to your reference genome (and their pair in the case of paired end and mate-pair sequencing) rather than performing these functions on the fastq files you get from the gsaf.
Unfortunatly, at the time of this class, velvet is not available on lonestar5. While we hope and think that this may just be because lonestar5 is very new still and it just hasn't happened yet, there is obviously no guarantee that it will come online as a module or a timeframe for when that may happen. Luckily (but somewhat annoyingly) it is available as a module on stampede. As we have discussed in class, stampede compute nodes are not able to access the BioITeam repositories so you will have to make sure you have copied your files to the locations you want them before you enter an idev node.
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