Attendance of this meeting is free, except for possible charges for any group lunch/coffee consumption. However, travel and accommodation cost must be covered personally; some help for transatlantic travel may be available from Chris Jiggins’s BBSRC meeting grant. A block of rooms will be reserved at the nearby Sheraton Commander Hotel from the evening of the 11th to the morning of the 14th. Harvard has discount with the Sheraton Commander of $199.00/per night. For more information please visit http://www.starwoodhotels.com/sheraton/index.html. If you would like us to add you to the reservation list please include a note to that effect when submitting your registration confirmation. If you do not included that you would like to be added to the reservation list we will assume that you will be making other accommodations for your stay and a room will not be reserved for you.

Some other lodging possibilities include the very conveniently located Irving House at Harvard, http://irvinghouse.com/about/story/ . This offers a range of rooming options with nightly costs upwards from $135.00 a night. If you are looking for something more cost efficient please consider searching for a room in a local shared apartment or house on Airbnb, https://www.airbnb.com/. This is also a good resource if you are traveling with a group that would like to “rent” the entirety of a private residence for the duration of your stay.

For the first day (morning of 12th) at least, there will be a limited number of talk slots available over the course of the meeting. If you would like to present a talk at the meeting please include a working title for your talk and a brief description of the talk with your registration confirmation. Please note talk slots will be filled on a first-come first-serve basis, with some preference given to active or recent work from each group internationally. After the talks we will arrange free periods for discussion of future directions in genomics and other international collaborative ventures.

Please send all attendance confirmations, including if you would like to have a room reserved and your talk information to Nikki Hughes, nhughes@fas.harvard.edu, no later than May 30, 2013. If you have any question or concerns, do not hesitate to direct your inquiries to Nikki at the email address above or at 617-495-0508.

Look forward to seeing you all in July.

Regards,

Nikki Hughes and Jim Mallet

We still have a ton of alignment problems, but this is the best I could come up with. It allows more mismatches, a little less so in the seed (that could probably stand to be relaxed). This also increases the gap parameters, but BWA still performs poorly in that respect. Based on what I have read, BWA really is not designed for this level of divergence and we see a lot of coverage gaps across the reference. For now I think we are stuck with this until we have an erato genome.

What parameters are you using for BWA that work well in erato?

I think including GATK in the assessment is useful if that is the SNP caller used downstream (it is for me). It is important how well the two work together.

As for further testing of aligners, I think this is only useful if we can generate some sort of “golden set” with known, or at least high confidence, answers.

I think simulations could be useful to give us a known answer and allow us to address some of the known issues. Although there are always caveats and biases.

We are attempting to improve alignments with de novo assembly and if it works, that may be useful to get us at least closer to a golden set. Of course you are then adding assembler biases into the mix.