Andor Kiss

Andor Kiss

Oxford, Ohio, USA

Miami University

Dr.

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Published on Sep 25, 2020

Annotation Update

No doubt we lost some time with the whole COVID-19 mess and the shutdowns; but we're through the RepeatModeler and RepeatMasker is finishing up; unmasked BUSCO complete genes are at 55%, which is p...

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Published on Feb 19, 2020

QC'ing & Diploid aware assemblies

QC'ing & Diploid aware assembliesWe're moving through "playing", or rather evaluating assembly parameters for the haploid version and assesing the quality of the assembly by comparing and contr...

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Published on Dec 08, 2019

Assembly Complete; onto polishing and BUSCO QC'ing

Using two SMRT cells (PacBio SII) worth of long-read data (N50 > 32,000 bp) we opted to use the wtdbg2 redbean (https://github.com/ruanjue/wtdbg2) assembler, we have assembled the wood frog geno...

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Published on Aug 11, 2017

First Assembly is Done!

First assembly of the wood frog genome is done! 8.6 G Bp - that's 2.5x the size of the human genome. We've done the initial sequencing run using the minION nanopore sequencer that produces ultra ...

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Published on May 12, 2015

Interesting XPrize - Consider Voting for Cryopreservation

Here's a opportunity to vote for an upcoming "Grand Challenge" for the XPrize: http://www.xprize.org/prizes/future-prizes/cryopreservation#.VVEhEG1euyc.facebook

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Published on Jan 23, 2015

Good News / Bad News (not really)

Just wanted to give everyone a heads up on a new development that's just come about. The company that sells/sold the kit (Illumina) has just announced a new iteration of their DNA sequencing machi...

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Published on Jan 05, 2015

Update - WF Genome

Hello,  We have obtained the kit from Illumina and are in the process of building the sequencing library.  I have also recruited three undergraduates to help with the annotation.  We hope to genera...

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Published on Nov 01, 2014

Thanks!

Hello,  Thanks to everyone that pledged!  With help from Illumina and all of you we hit our goal!  I'll be keeping everyone posted on the project.Regards,Andor

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Published on Oct 31, 2014

Lower Budget!

Hi Everyone,  Some good news - I've been working with Illumina and they've been able to lower the cost of the reagents by $750 - that brings our overall budget down to $3000!  AND much closer to o...

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Yeah, we got about 3x coverage with nanopore (30 kbp - 90 kbp), and ~27x coverage with PacBioSII (N50 >32kbp) and we're just waiting for a complete lane of HiSeq3000 150 bp PE so that we can try an assembly that will polish the long PacBio reads with a hybrid assembler. We should have a good quality, polished assembly, annotated (with transcriptome data) sometime late January 2020. Basically, it's all sequenced, and we're in the middle of doing the combined assembly - we needed to build out a complete heavy duty workstation to do this - but we have it and we're in the home stretch.
Nov 27, 2019
Unlock the Secrets of Animals that Survive Freezing!
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Rather, it should read "...it does not do novel and complicated..."
Aug 23, 2017
Unlock the Secrets of Animals that Survive Freezing!
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The problem is not cheap per se, but rather how to do it well. Human genome re-sequencing is relatively easy, as one is mapping to a reference. De novo assembly from short-reads into coherent scaffolds is a whole different problem. Additionally, BGI does straight-forward sequencing projects very well, it does do novel and complicated projects well. And this is what we are doing. We may have them fill in some of the gaps with HiSeq3000/4000, but I suspect that they won't have better approaches than US based facilities.
Aug 23, 2017
Unlock the Secrets of Animals that Survive Freezing!
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Hi Aaron, We're going to get started this summer. There was an intentional delay in the start of the project as Illumina introduced their new high capacity HiSeq3000 and HiSeq4000 instruments. There was also time needed to let these instruments find their way to university core-labs. Now that this has happened, we're going to start the process.
Apr 26, 2016
Unlock the Secrets of Animals that Survive Freezing!
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Hi Andrew, Thanks for the pledge & thanks fro the suggestion of slashdot & BoingBoing. I contacted NPR, but so far no response. - Andor
Oct 27, 2014
Unlock the Secrets of Animals that Survive Freezing!
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Thanks David - yes, I think the frog has a lot to teach us about cold and freezing strategies.
Oct 13, 2014
Unlock the Secrets of Animals that Survive Freezing!
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Met with people from NSF - very encouraging
Oct 05, 2014
Unlock the Secrets of Animals that Survive Freezing!
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Good Luck!
Oct 03, 2014
Penang Seahorse Survey
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Good Luck
Sep 30, 2014
Unlock the Secrets of Animals that Survive Freezing!
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