Readers may keep an eye on #SMRTBFX hashtag on twitter to follow an ongoing conference. This is the best place to know about the latest bioinformatics algorithms on long reads.
Gene Myers is again the star of the show. He has been distributing a lot of goodies through his Dazzlerblog, such as -
dasDAS – The Dagstuhl Assembly Spec
Jason Chin, Richard Durbin, and myself found ourselves together at a workshop meeting in Dagstuhl Germany at the end of August and hammered out an initial proposal for an assembly format that we think is quite comprehensive and general purpose.
Morever, while damapper will run in any reasonable (e.g. 16Gb) amount of memory, it runs faster the more memory there is available. For example, with 48Gb, damapper is 1.8 times faster than BWA on the human genome, 15 times faster on the fly genome, and 36 times faster on E.Coli. Performance will be reported on more extensively in a subsequent post.
Seeing Your Reads: DaViewer
In brief, DaViewer allows you to view any subset of the information in a given .las file of local alignments computed by the daligner or the forth coming damapper, and any track information associated with the read database(s) that were compared to produce the local alignments (LAs).
We will post other highlights from the meeting by updating this blog post.
Keynote speaker: Gene Myers, Ph.D., Max Planck Institute Confirmed speakers: Kin Fai Au, Ph.D., University of Iowa Ali Bashir, Ph.D., Mount Sinai School of Medicine Brett Bowman, PacBio Andrew Carroll, Ph.D., DNAnexus Jason Chin, Ph.D., PacBio Richard Hall, Ph.D., PacBio Alex Hastie, Ph.D., BioNano Genomics Aaron Klammer, Ph.D., PacBio Sergey Koren, Ph.D., National Human Genome Research Institute Maria Nattestad, Cold Spring Harbor Laboratory Nik Putnam, Ph.D., Dovetail Mike Schatz, Ph.D., Johns Hopkins University Yuta Suzuki, Ph.D., University of Tokyo Elizabeth Tseng, Ph.D., PacBio Aleksey Zimin, Ph.D., University of Maryland
(ii) Sergey Koren spoke about Canu assembler
(iii) Jason Chin’s talk was on FALCON assembler
(iv) Elizabeth Tseng spoke about ‘Iso-Seq and beyond’
Slides here at Dropbox.
(v) Brett Bowman discussed ‘16-point HLA Typing with Long Amplicon Analysis v2’
The slides are available here.
(vi) Lance Hepler’s talk is on ‘CCS2 - of statistical might and scientific magic’
The slides are available here
Many thanks to Liz Tseng (@magdoll) for providing all links.