Postdoc @ JHU w/ Steven Salzberg
Baltimore, MD
Joined February 2012
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Florian Breitwieser retweeted
Visualize your metagenomic sequences with Pavian, developed by my (now former) postdoc Florian Breitwieser. The software came out long ago, but (finally) the paper is out too academic.oup.com/bioinformat…
Florian Breitwieser retweeted
For those who want the supplemental materials and can't wait for the full paper to appear, I've put them on my ftp site for anyone to download: ftp://ftp.ccb.jhu.edu/pub/salzberg/Contaminated_genomes_GenomeResearchPaper_2019/ – at New York, USA
Florian Breitwieser retweeted
Real-time measurement of protein–protein interactions at single-molecule resolution using a biological nanopore: nature.com/articles/nbt.4316
If anyone needs a quick alignment coverage calculation + visualization on the terminal, the tool `bamcov` is now available at github.com/fbreitwieser/bamc…
Florian Breitwieser retweeted
We've released another Kraken (KrakenUniq, just published) Very elegant work by @fbreitw using randomized counting algorithm to enhance the Kraken metagenomics software. #microbiome genomebiology.biomedcentral.…
Florian Breitwieser retweeted
KrakenUniq (formerly KrakenHLL): confident and fast metagenomics classification using unique k -mer counts
genomebiology.biomedcentral.…
github.com/fbreitwieser/krak…
Florian Breitwieser retweeted
Fantastic keynote talk at #biodata18 by @StevenSalzberg1 from @JohnsHopkins on adventures and misadventures in genome data mining with lots of fun stories about horizontal gene transfer. #blastology #hgt #genomics #datamining
The MicrobeScope – Infectious Diseases in Context informationisbeautiful.net/v… via @infobeautiful
Florian Breitwieser retweeted
My entry for the May #SWDChallenge is a waterfall chart showing how the budgets of 18 US federal departments changed from 2017 to 2018, effectively transferring funding from 15 departments to 3. cc @storywithdata
Florian Breitwieser retweeted
New paper in press today at @NatureRevGenet: Piercing the dark matter: bioinformatics of long-range sequencing and mapping rdcu.be/J8Ib. Summarizes all the major ways long reads, linked reads, HiC and Optical Mapping are being used to advance genomics
Florian Breitwieser retweeted
just making my way through it now. this is great, almost reads like a new manuscript. the bits about kmer to read ratio and the demonstration of how that relates to confidence in a true species call = great work. thanks for the update!
Florian Breitwieser retweeted
In our new metagenomics program KrakenHLL: probabilistic counting lets us count unique k-mers with remarkably little memory. Who knew that a hashing algorithm (#HyperLogLog) could be a hashtag too? biorxiv.org/content/early/20…
Florian Breitwieser retweeted
Removing Contaminants from Metagenomic Databases biorxiv.org/content/early/20… clean genomes: ccb.jhu.edu/data/eupathDB/
Florian Breitwieser retweeted
KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts from @fbreitw and @StevenSalzberg1 biorxiv.org/content/early/20… code github.com/fbreitwieser/krak… cc @KristaTernus @brooksph @ctitusbrown @traingene
Florian Breitwieser retweeted
KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Florian Breitwieser retweeted
Looking for postdocs to join Kim lab kim-lab.org working on graph alignment, HISAT3, and other projects. kim-lab.org/open-positions
Florian Breitwieser retweeted
I submitted NGMLR + Sniffles preprint to a bioinformatics peer price. Illustrating an advance long read mapping and SVs calling using @Pacbio / @nanopore and probes systematic errors in short read SV calling.
Please vote + RT:
thinkable.org/submission_ent…
@philres1 @mike_schatz
Florian Breitwieser retweeted
Who is interested in SVs, human genomics/clinical data, Texas, can program and has a PhD? Lets work together! Apply:
fritzsedlazeck.github.io
Florian Breitwieser retweeted
With so much talk of corp tax cuts, thought it was interesting that median effective tax rate for $spx is near a record low @NDR_Research
Florian Breitwieser retweeted
Have been looking forward to this paper from @infphilo and @StevenSalzberg1 biorxiv.org/content/biorxiv/… FM index based metagenomic classificn