I need help on visualizing a microbial genome sequence obtained from Miseq-paired end reads. I am not sure, when using the tools, how the input file should look.
Can anyone help me with generating the input files? I did go through the ggbio manual, so if anyone could point out the steps to generate the files to be loaded into the respective software, that would be great.
if its only visualisation you can just use something like Ugene installed on your OS of choice.
This is assuming you have contigs done and orf reading done.
Sorry to mention, I am not at the initial stages with raw reads. The sequences were filtered and trimmed prior to assembly with atleast 4 differnt assembly softwares after kmer optimization and N50 value. And the generated contigs were ordered with CISA. The contigs files were also annotated using the RAST server following orf finds and other steps. I have in my hand output as the GFF, Genbank etc annotation files which are generated by the seed system.
Using CIRCOS for bacterial genomes is actually trivial. Just remember that using CIRCOS itself requires you to manipulate multiple files, so the learning curve is a bit steep, but it is well worth the final results. See a few useful links here.
http://circos.ca/documentation/tutorials/2d_tracks/text_1/
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