quick memo for genome assembly workshop

@assemblathon

First talk of the Genome Assembly Workshop (#gaw) meeting will be Richard Durbin from the Wellcome Trust Sanger Institute

@assemblathon

About a 100 people here for the #gaw meeting and also for the @genome10K meeting that follows

Keith Bradnam 📈 @kbradnam

I'm sort of live tweeting in my role of @assemblathon co-organizer at the Genome Assembly Workshop (#gaw) in Santa Cruz.

BGI Group @TheBgiGroup

Start of the #gaw (@Assemblathon) part of the @Genome10K meeting, Richard Durbin starting proceedings talking about SeQuence Graph format

GigaScience @GigaScience

Including us... RT @assemblathon About a 100 people here for the #gaw meeting and also for the @genome10K meeting that follows

@assemblathon

Richard Durbin is talking about an idea for standardizing an assembly graph format #gaw

BGI Group @TheBgiGroup

RD giving some assembly issue background: 10-15% of genome cannot be reliably mapped to. Most false positives come from mapping errors. #gaw

GigaScience @GigaScience

Richard Durbin talking about formats (BAM, etc.), and standardizing an assembly graph format in his talk on SeQuence Graph (SQG) #gaw

GigaScience @GigaScience

RD: lots of the desired tools outlined developed to some extent by Amos http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS #gaw

@assemblathon

Good question about how more advanced genome file formats may not always be as intuitive for a typical user of data #gaw

BGI Group @TheBgiGroup

Now its time to assess the state of the art in genome assembly. Ian Korf up now to give the results of the @Assemblathon #gaw

BGI Group @TheBgiGroup

Ian Korf: @Assemblathon stats first: 7 countries. 17 teams. 62 assemblies. >100 metrics. So much data, had to be sent on hard disks. #gaw

BGI Group @TheBgiGroup

Contamination part of @Assemblathon challenge “all libraries will contain some bacterial contamination” – 5% of seq was from E. Coli #gaw

Deanna Church (she/her) @deannachurch

You can see the results from the Assemblathan here: http://tinyurl.com/4cpr9xv #gaw #DataOverload

The Assemblathon @assemblathon

A PDF of my talk (with notes) is now up on the Assemblathon website http://t.co/LxLWwOP #gaw

Dawei Lin @iGenomics

Assemblers have invented sequences not exist in either haplotypes used in the contest. #assemblathon #gaw

The Assemblathon @assemblathon

“@iGenomics: Assemblers have invented sequences not exist in either haplotypes used in the contest. #assemblathon #gaw”

BGI Group @TheBgiGroup

From @kbradnam RT @assemblathon A PDF of my talk (with notes) is now up on the Assemblathon website assemblathon.org/pages/results #gaw

Dawei Lin @iGenomics

Hap path gives no penalty to switch haplotypes but does count for inconsistent haplotype blocks in the assemblies #assemblathon #gaw

Dawei Lin @iGenomics

Nearly all assemblies had excellent coverage (reads are all mostly mappable) # assemblathon #gaw

Dawei Lin @iGenomics

Ian has been using his iPhone as his text prompter. #assemblathon #gaw

Deanna Church (she/her) @deannachurch

Next: David Jaffe and Sante Gnerre ALLPATHS-LG "good cheep assemblies" #gaw #assemblathon

Dawei Lin @iGenomics

David Jaffe is talking about ALLPATH-LG. 29genomes sequenced by capillary technology cost about ~$20M per genome. #gaw

BGI Group @TheBgiGroup

Up now is David Jaffe/Sante Gnerre from @broadinstitute with "ALLPATHS-LG: good cheap genome assemblies" #assemblathon #gaw

Deanna Church (she/her) @deannachurch

SG: Needed new computational methods and new laboratory methods. #gaw #assemblathon // assembly is not just an algorithmic problem!!