i5K Project Status Updates
January 8, 2013
By: Fringy Richards
Welcome to the New Year—and my late end of year update!
We now have DNA for all but 4 of the 33 species, and know that 2 are in inbreeding, Although some will need trouble shooting, so all is going well for DNA collection .
Library construction and sequencing is going well, and the library group can see the end of the project in terms of species going through their hands.
Sequencing is keeping up, so I expect that the assembly and annotation processes are going to be the bottlenecks for the project in terms of getting data into everybody's hands.
We now have 7 species where the assembly process has at least started. In general we will get good assemblies for the project, but it is clear there will always be some problematic species.
The medfly and sawfly have excellent assemblies, the house spider is also finished and has an OK assembly (10kb contig N50), the asian long horned beetle will have a 10-15kb contig N50, the psyllid DNA came from multiple individuals, ended up with a 2.4kb contig N50, and needs a plan B (I am thinking about that) the black widow unfortunately has a smaller N50 than I had expected as it came mostly from a single individual—5kb contig N50—and so I am thinking about how to get this up to 10kb to make it publishable, finally the bedbug assembly is running.
At least for now the genome sequences are coming in faster than the assembly pipe can handle, but we are making progress, and I am confident we will have all of the assemblies finished in 2013—hopefully in the first half—but possibly in the first 9 months.
Finally I should make my New Years resolutions for the project—I hope to be putting all of the data on the website as soon as possible, so you can see everything we can see. Our to-do list includes blast access to all of the sequences, and finally we are still looking to hire someone to do the annotation for these genomes, so please email me if you are interested in that job.
Cheers, and best for 2013!
November 12, 2012
By: Fringy Richards
We now have DNA for all but 8 of the 33 species, and know that 2 are in inbreeding, that one is coming soon, and need to poke the remaining groups who have promised us DNA soon.
Of the 25 species with DNA in-house, libraries have been ordered for 22 species.
The library group has started on or finished libraries for 15 species. Of these 15 species, sequencing has been started on 11 species. Of these 11 species where sequencing has started, 6 are complete:
Asian long-horned beetle
Common house spider
Hackberry petiole gall psyllid
Western Black Widow
Of these, 4 are in the assembly process, and 1, the medfly, has finished assembly and needs to have the assembly readme made and the data put on the website.
The medfly is our first assembly. I can now report to Al, Marc, and everyone in Italy, that it looks great, and that your inbreeding paid off. The contig N50 is 46kb, and the scaffold N50 is 4Mb.
October 2, 2012
Not too much has changed from last week.
The common house spider is in the middle of a test assembly, and the medfly is being prepared for assembly. I am anxious to see how these come out. On the website front, we have added data storage places with links from the species table, although very few of them have data yet—we are beginning to fill them up.
So far the only one with any data is the medfly.
You can see the links on the right hand side of the species table.
Each data link goes to five directories.
Some data for the medfly is now in the genomic directory.
(We are in the process of tidying up the names, so things may change a bit.)
Finally, I think we are in contact with everyone about the remaining DNAs, although my never ending struggle with email may mean I am behind talking to some of you.
(Sorry Georg, amongst others) Of the species where we need DNA I think we have a good handle on the wait for the stink bug, lucerne flea, milkweed bug, sheep blowfly, velvet worm and water strider.
Specific Updates Needed, Please.
I still need to talk with Helen about Hyalella, Sean about the Mantisfly, and perhaps Cody about the cockroach. Otherwise I think that—assuming the assemblies work out OK—everything is going rather well, and we just have to keep the ball rolling.