Florian Breitwieser

Postdoc @ JHU w/ Steven Salzberg

[Steven Salzberg 💙💛 @StevenSalzberg1]

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 https://t.co/o1xM85rwFW

[Florian Breitwieser @fbreitw]

@TSydenhamDK @StevenSalzberg1 Thanks a lot for responding so quickly! We had hoped that our publication would lead to that.

[Steven Salzberg 💙💛 @StevenSalzberg1]

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/

[Winston Timp @timp0]

Real-time measurement of protein–protein interactions at single-molecule resolution using a biological nanopore: https://t.co/QLZqFIZ7tU

[Florian Breitwieser @fbreitw]

If anyone needs a quick alignment coverage calculation + visualization on the terminal, the tool `bamcov` is now available at https://t.co/Z4ErY8XSnD

[Florian Breitwieser @fbreitw]

@Seb_Matamoros The method was developed independently from Kraken 2. Once Kraken 2 is published, we may develop a -Uniq version of it, too. KrakenUniq supports Kraken 1 databases, though, as well as building new databases with extended taxonomy.

[Steven Salzberg 💙💛 @StevenSalzberg1]

We've released another Kraken (KrakenUniq, just published) Very elegant work by @fbreitw using randomized counting algorithm to enhance the Kraken metagenomics software. #microbiome https://t.co/bgwUeJrik7

[Stephen Turner 🦋 @stephenturner.us @strnr]

KrakenUniq (formerly KrakenHLL): confident and fast metagenomics classification using unique k -mer counts
https://t.co/l0bvWnCmsB
https://t.co/FSN9xllabm

[Florian Breitwieser @fbreitw]

@sedlazeck Indeed! @samkovaka

[Meghan Ferrall-Fairbanks @DrMeghanFerrall]

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

[Florian Breitwieser @fbreitw]

The MicrobeScope – Infectious Diseases in Context https://t.co/gehLsTqRgx via @infobeautiful

[Florian Breitwieser @fbreitw]

@timelyportfolio @dataandme @chenxingus @theduncanclark @f_l_o_u_r_i_s_h @timelyportfolio has a great selection of D3 viz packages! The first version of my hierarchical visualization R package is available at https://t.co/TLnrXlfcbF

[Ben Jones @DataRemixed]

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

[Michael Schatz @mike_schatz]

New paper in press today at @NatureRevGenet: Piercing the dark matter: bioinformatics of long-range sequencing and mapping https://t.co/58xKPpfMab. Summarizes all the major ways long reads, linked reads, HiC and Optical Mapping are being used to advance genomics

[Stephen Turner 🦋 @stephenturner.us @strnr]

@KristaTernus @fbreitw @StevenSalzberg1 @brooksph @ctitusbrown @traingene 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 @fbreitw]

@AdamBazinet Thanks @AdamBazinet ! Yes, you can use it as drop-in replacement for Kraken - if used on the same database it provides three additional columns in the report with info on the k-mer counts. Jen Lu made the new format work with Bracken, too

[Florian Breitwieser @fbreitw]

@devindrown @gringene_bio @rec3141 I think you should be able to get a Kraken-style report from kaiju by running `kraken-report` on the kaiju output. Thanks for reminding me of the issue, see https://t.co/0LecVXGeNZ

[Steven Salzberg 💙💛 @StevenSalzberg1]

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? https://t.co/kVF0DByGyf

[Stephen Turner 🦋 @stephenturner.us @strnr]

Removing Contaminants from Metagenomic Databases https://t.co/2bnePecBFc clean genomes: https://t.co/KdKI8ncaXV

[Stephen Turner 🦋 @stephenturner.us @strnr]

KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts from @fbreitw and @StevenSalzberg1 https://t.co/P4XgrTZSUV code https://t.co/CvNQCqImPx cc @KristaTernus @brooksph @ctitusbrown @traingene