Tim Amos

Bioinformatics Engineer at @GarvanInstitute

[Genomic Technologies Group @GenTechGp]

Come join us this November 13th for the Garvan Long-Read Research Symposium! You'll hear about the wonderful things you can do with @nanopore and @PacBio long reads from a great line-up of speakers. FREE to attend. Register below
https://t.co/vMc0x3mwmz

[Hasindu Gamaarachchi @Hasindu2008]

Introducing cornetto, an adaptive genome assembly paradigm using @nanopore adaptive sampling.
- greatly reduces cost per genome assembly
- reference agnostic, so works for non-humans
- assembly just using saliva
- & many more
Relies on 2 excellent software #readfish & #hifiasm.

[Genomic Technologies Group @GenTechGp]

Not long now until the @GarvanInstitute Long Read Research Symposium on November 7th. We will have talented speakers covering the advantages of both @nanopore and @PacBio data
Only a few spots left - don't miss out! 💃
https://t.co/fvgVtzOpfs

[Heng Li @lh3lh3]

I was one of @Hasindu2008's thesis examiners and had email exchanges with him later. If I were to optimize nanopore basecalling, I would take an approach similar to his SLOW5 format & associated tools. That is engineering done right, IMHO.
https://t.co/zqG0MkUlCU

[Tim Amos @amos_tim]

We now use Buttery-eel exclusively in our Nanopore sequencing service for all rebasecalling (e.g. super accuracy). I found it easy to install and use. @jamfer is also responsive to feedback, at least from me, so let him know, if you have any.

[Genomic Technologies Group @GenTechGp]

Buttery-eel is a new tool that allows you use @nanopore's Guppy basecaller with SLOW5 input files. Why would you do that? Because it's fast! Another nice addition to the SLOW5 ecosystem from @hiruna72 @Hasindu2008 @Psy_Fer_ 🐍🧈🐍🧈

https://t.co/YQcLdHtrs7

[Tim Amos @amos_tim]

The 3 reasons my 5 year old gave this evening for why she loves me:
1. Because my name starts with T
2. Because I'm her father
3. Because I gave her DNA

[Tim Amos @amos_tim]

Basecalling of #SLOW5 using #Guppy (the normal #nanopore basecaller) is now available for everyone (our lab had it working earlier but couldn't share that method because of IP restrictions).

[James Ferguson @Psy_Fer_]

Ever wanted to basecall SLOW5 files with guppy?

Your wish has been granted!
@Hasindu2008 and I are happy to introduce:

The buttery-eel - a slow5 guppy basecaller wrapper

https://t.co/6VH7N6cDWG

[Tim Amos @amos_tim]

@cabbagesofdoom Not sure. pdfgrep might at least allow you to skip a manual copy and paste step. I use it to extract specific lines from a table in a pdf.

[Dr Laura Sharpe @laurajsharpey]

Who else is ready for their election party?
@AusElectoralCom

#AusVotes2022 #democracysausage #DemocracyCake

[James Ferguson @Psy_Fer_]

Ever thought: "I really wish @nanopore bonito basecalling was faster, especially when running multiple datasets at once"

We have, and by integrating slow5 via pyslow5 into bonito, we have sped up parallel runs, especially under heavy load, by a fair bit
Give it a try, link below

[Tim Amos @amos_tim]

I keep describing this work when I want an example of an exciting use of @nanopore

[Genomic Technologies Group @GenTechGp]

We used ReadUntil targeted @nanopore sequencing to solve tricky tandem repeat disorders. Read all about it: https://t.co/jOGYMhrmn1

[James Ferguson @Psy_Fer_]

Introducing SLOW5, a new file format to solve the issues of multithreading and parallel data access present in the @nanopore FAST5 (HDF5 lib) format. With SLOW5, we show a speed up of ~30x for WGS methylation calling and a ~25% reduced data storage footprint. 1/9

[Genomic Technologies Group @GenTechGp]

We're recruiting a new lab scientist role. 🧑‍🔬🧬🦠
Work on long-read sequencing projects solving human disease, viral surveillance & vertebrate genome evolution & learn from @nanopore gurus such as @jil_hammond & @Psy_Fer_.
🚀 Interested? https://t.co/gg8sz0skAB

[Tim Amos @amos_tim]

@BioMickWatson Musk said that he'll use methane made from CO2 using solar to fuel his new rocket thus making it indirectly powered by renewable energy. If he does this, then his plans to replace intercontinental flights with this rocket will actually lead to less burning of long dead biomass.

[Tim Amos @amos_tim]

@spudiscool I like my home made standing desk (chest of drawers with the screen on a pile of books on the window sill behind it) that I've been using all pandemic. I do use a smaller screen than I would otherwise though because I have to move it to shut the curtain every night.

[Tim Amos @amos_tim]

@cabbagesofdoom Agreed. Plastic bags can also be recycled at Coles and Woolies. Going to a supermarket does feel icky during a pandemic but going when it's not busy and wearing a mask keeps the risk down. Likewise, refusing plastic bags is great but also can feel less hygienic during a pandemic.

[Tim Amos @amos_tim]

My five year old son when reading a book to me: "policeman? We call it a police officer because women can be police officers too" #littlefeminist @manwhohasitall

[Tim Amos @amos_tim]

@spudiscool If I wrote a bit of code I'm proud of or think is cool, I totally share it with a colleague. There's plenty to learn in both directions from sharing your code and "code reviews" even if ad hoc and informal. My JavaScript is likely too rusty for this case though.

[Garvan Institute of Medical Research @GarvanInstitute]

A team led by Dr Ira Deveson developed an app called ‘Genopo’ that can analyse the coronavirus genome on a smartphone in less than half an hour. This will make genomics more accessible to remote or under-resourced regions. https://t.co/xXnPIDCUNc @nanopore @GenTechGp

[Tim Amos @amos_tim]

@phatmattbaker @cabbagesofdoom @ScienceMagazine Fair enough, just because I could identify one contributing factor doesn't mean it's a major one. I imagine that systemic racism plays an important role but I should be careful not to pretend I know more than I do.