Hey everyone,
I'm not sure how many people know about this, and presumably even fewer could have CLC to try it, but two days ago I noticed that CLC has a beta version of a plugin for Genomics Workbench that is supposed to help you finish off a genome using paired read data, primarily from the MiSeq it appears. From the available tutorial it seems like it relies heavily on contig alignment and trying to use pair distances to bridge contigs, which is something that I've been manually doing in an attempt to close the genome for the primary strain we use for making mutants.
There's a trial of the plugin that I'm planning on testing, but I wanted to see if anyone else has tried it and what their impressions are. It's not going to be a free plugin, so I'm wondering how well it works and whether or not it would ultimately be worth the price (which I've yet to get a quote for) compared to what I've been doing manually myself.
There also is a blast2GO plugin that's in beta and is similarly not going to be free, for those that care to know. Not sure how much it extends the standard blast2GO or if it's mostly to integrate annotation into CLC's GUI interface.
I'm not sure how many people know about this, and presumably even fewer could have CLC to try it, but two days ago I noticed that CLC has a beta version of a plugin for Genomics Workbench that is supposed to help you finish off a genome using paired read data, primarily from the MiSeq it appears. From the available tutorial it seems like it relies heavily on contig alignment and trying to use pair distances to bridge contigs, which is something that I've been manually doing in an attempt to close the genome for the primary strain we use for making mutants.
There's a trial of the plugin that I'm planning on testing, but I wanted to see if anyone else has tried it and what their impressions are. It's not going to be a free plugin, so I'm wondering how well it works and whether or not it would ultimately be worth the price (which I've yet to get a quote for) compared to what I've been doing manually myself.
There also is a blast2GO plugin that's in beta and is similarly not going to be free, for those that care to know. Not sure how much it extends the standard blast2GO or if it's mostly to integrate annotation into CLC's GUI interface.