Forum: Plant And Animal Genome XXVII (PAGXXVII) highlights thread
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4.5 years ago by
Philipp Bayer6.7k
Philipp Bayer6.7k wrote:

PAGXXVII (Plant And Animal Genome XXVII) is over and it was as usual an extremely dense program, meeting after meeting - I thought I'd collect some of my highlights so that others could contribute theirs, so that together we can paint a more complete picture of what was of interest.

- NRGene assemblies were featured in many plant genome talks - it looks like using only paired end/mate-paired data in varying insert sizes with some huge coverage (180x to 250x IIRC) you can get N50s of complex plant genomes like wheat in the range of 50 to 100 Mbp. The comparison to the published wheat chromosome 3B was pretty good with some minor problems (IIRC about 5% chimeric contigs). See this abstract or this abstract for example. It's closed source, the company runs the assembly for you, apparently in only a few days/weeks. I assume that's why it's called DeNovoMAGIC.

- The IWGSC Standards & Protocols workshop had interesting new software from Philippe Rigault at GYDLE to assemble BAC-contigs and assess & fix them using BioNano maps, but the software isn't available yet (no abstract either), IMHO it looked like early stage but very promising

- The combination of PacBio reads + BioNano maps + HiC scaffolding looks great, see for example the numbers in Sergey Koren's slides

- The Exhibition Hall had a PacBio Sequel and an Oxford Nanopore PromethION machine, both very cool

- Jason Chin (@infoecho) presented news on the FALCON assembler (slides here), the same session presented news on the PacBio SMRT Analysis software (next version uses bam files instead of h5 files!)

- PacBio also presented their SMRT grant, application-deadline is soon on the 31st: If you win with your interesting genome you get one library prep + sequencing + assembly + bioinformatics analysis

- John Quackenbush's (@johnquackenbush) plenary talk had some interesting graph-based approaches to GWAS SNP meta-studies (paper), definitely something to follow up

- Weibo Xie presented this paper on rice metagenome assembly at the Rice Informatics Workshop: Very interesting!

- At the same session I presented a very early start to connect all the different Information Systems and data exchanges (wheatIS, legumeIS, International Rice Informatics Consortium, DivSeek etc.) under an "AgbioData" umbrella, not (yet?) to connect all these databases, but to at least connect the people in the various initiatives so that they know who to talk to and not to duplicate too much work between the initiatives. It's all very early, we only started talks at this PAG.

I was in a ton of meetings so my highlights are a bit thin and I'm sure I forgot half of it, maybe you guys have more?

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