Professor
@hi
.is in CS, head of rna seq data analysis at decode genetics (views are mine). Bioinformatician, epistemic trespasser, &c. ps. I hate GTF files
In this preprint with
@sindri_e
we compared seven widely used methods for batch correction of single cell RNA-seq data. We found that all but one of the methods introduce batch effects when there are none. 1/N
Exactly one month ago Iceland had 1045 active diagnosed infections. Today we have 99 active, and added 608 new cases during this time, most of which have recovered.
#TestTraceIsolate
New release of kallisto is out
kallisto can now produce BAM files in genomic coordinates, sorted and indexed for IGV consumption, details in a new blogpost
Oh, and it runs on a tiny computer
Speed is crucial in fighting this epidemic. In Iceland we use test-trace-isolate to curb the spread in addition to restrictions on social gathering, 2m social distancing and mask wearing in public.
Here is a rough timeline of what happens for a positive diagnosis
New preprint out w
@lpachter
&
@vntranos
on the Barcode, UMI, Set format (BUS) for processing of single cell RNA-Seq datasets. Shows how to create modular frameworks for processing scRNA-Seq data, fast using kallisto (v 0.45.0 just released) and simple
deCODE genetics is has stepped up to assist with covid19 screening in Iceland. Started last Friday and have completed 1800 tests and are operating at a rate of 1000 tests per day. That’s 0.3% of the population per day.
Border screening in Iceland has detected 13 cases of the British variant. Twelve came from the UK, one from Denmark. Every positive sample is sequenced.
Gene databases: so there is this gene called LAMP3
Me: sounds good
Gene db: but wait there is also CD63
Me: ok?
Gene db: and it’s also known as LAMP-3, I mean what could go wrong
Me: [...]
Iceland has found 12 cases of omicron confirmed with sequencing. All PCR positive cases are sequenced. Since the first report of omicron, all S dropouts have been sequenced within 24 hours. The US has confirmed 20 cases, how large is the the iceberg?
Yesterday was my 10 year anniversary in bioinformatics. Thanks to
@jkpritch
for taking a chance on me when I knew nothing about genomics, sequencing, and rna. Heading out to
#ASHG19
now
The paper is the result of this thread pulling. My advice is twofold and simple.
1. just use Harmony
2. if you are correcting for batch effects, make sure it does nothing when there are no batch effects.
9/N (N=9)
Triple blind review.
Authors don’t know the identity of reviewers and vice versa. Reviewers don’t know the identity of the journal.
Should the quality of review and rigor depend on where it was submitted?
The paper from
@decodegenetics
on the spread of SARS-CoV-2 in the Icelandic population is finally out proud to have worked on this with
@hakon_jon
and others
Bifrost – Highly parallel construction and indexing of colored and compacted de Bruijn graphs. Paper by
@GuillaumOleSan
and myself, constructs colored de Bruijn graphs for 118K Salmonella strains. Software: , preprint:
I’m psyched about the vaccine lottery this week in Iceland. No $1M prize, we will randomly draw a birth year (1975-2005) and all born on that year will be vaccinated that time. And we’ll keep going till we’re done.
🤞1980
Genome informatics 2022 will be held as a hybrid conference in Hinxton, UK Sep 21-23 this year.
Right now you have one week to submit your abstract for
#GI2022
(deadline July 12th)
You know what to do.
We have a position available at the University of Iceland building up bioinformatics services as well as working on bioinformatics in my group. deadline is april 18th, plz retweet.
Yesterday Iceland received 10K doses of the Pfizer vaccine (for 5K people). Today 2.5K were vaccinated and we will finish the doses tomorrow. Throughput is estimated to be at least 10K per day.
Scaled up to the US this corresponds to 2.5M people.
New preprint out, lead by
@kreldjarn
&
@SolviStats
Two key results.
1. Reconstruction of a giant infection tree with 2500+ infected individuals from the "third wave" of covid in Iceland.
2. Using this tree to simulate the effect of vaccinations
1/5
I’ve written software that eats millions of reads in a matter of 10 seconds.
I don’t hesitate grepping huge files and feeding them into a series of pipes of awk/cut/sort/uniq that I write with my eyes closed.
But canvas takes 10 seconds to list discussion items 🤷
Setting up new computer:
0 min, where did all the brew packages go?
2 min, what is this bioconda thing I keep hearing of
5 min, why didn't anybody tell me about this thing before ?!?
I just had a covid test as a random sample from the population. I timed the visit, 4 minutes and 50 seconds from entering the building until walking out again. Results are promised within 24 hours, but I’m guessing I’ll know later tonight.
The data behind this figure is based on contact tracing for about 1200 individuals. Each trace requires about 20-200 phone calls and is done by a dedicated team at
@almannavarnir
working hard to contain the spread
The report from DeCode and Kari Stefansson is out.
"Spread of SARS-CoV-2 in the Icelandic Population"
They tested 6 % of Iceland population. Found 0.6-0.8% infected.
Charts show transition from imported case to family spread in a month.
A member of parliament in Iceland(stepping in as a substitute for another MP who is infected with Covid) is trying to get an isolation of Covid positive individuals thrown out in the courts.
Ironically, not for the MP he is substituting for.
1/4
Dear everybody,
If you have to choose one nice thing to do for the computer geek helping you, don't use spaces in your filenames.
Instead of "My Document", use "my-document", "my_document" or "myDocument"
Spaces indicate the end of the filename in some of the tools we use.
0.4% of all Icelanders were diagnosed PCR positive for Covid yesterday. Scaled to the US that’s like 1.5M in one day.
Elementary schools will open Jan 4th and 5-11y vaccinations will begin on Jan 10th. What could possibly go wrong.
@iddux
Bioinformatics algorithms by Pevzner and Compeau. The alignment chapter alone is worth it because it emphasizes understanding over implementation details. Rosalind problems are a fantastic addition to just studying the text
Contact tracing has significantly reduced the spread of the virus.
But it’s not enough by itself.
Do your part. Limit social interactions, wear a mask, get tested ASAP for symptoms
/end
My TEDx talk on the importance of building interpretable, open box machine learning models and using domain-informed detective work to accelerate discovery in genomics, biology, and medicine:
We argue that it is better to not modify the cell-by-gene matrix at all but rather to correct objects which affect clustering. Downstream statistical tests can then take the batch identifier as a covariate, e.g. linear models or MAST. 6/N
Very interesting analysis of the choices made when designing the Biontech/Pfizer mRNA vaccine. So much of this builds on top of decades of basic scientific research. Our public research funds hard at work.
That's a wrap for a great Genome Informatics conference
#gi2023
See you next year in Hinxton, UK
btw, the cover had a small easter egg, let me know if you can find it
.
@ggonnella
talking about GFA format , grew out of a blog post …,
@lh3lh3
proposed GFA in another blog post …, specification came later and improved to GFA2 which generalized better for long read technologies
#GI2018
This is really awesome! Next step is to just display a Shiny app where people can play with the data, and really interact with the story - not frozen figure images. The future looks cool 😎📊📈
I'll give a short talk on the value of sequencing all SARS-CoV-2 samples in Iceland as part of the
#COVID19Nordic
research response workshop
This Thurs with free reg
Great talks from all the Nordics detailing strategies for dealing with the epidemic
Yes we’re an island. Yes we are tiny. Reykjavík is not as dense as New York (but similar to urban US cities, eg Pittsburgh). Is it harder to scale this up? Yes, but totally worth it even if it is not 100% effective.
#TestTraceIsolate
+ quarantine close contacts.
I got my 3rd dose of vaccine (j&j, Moderna 100, Moderna 50) this morning. I can feel the aches starting up so now is a good time to grade that final exam.