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The MicrobeScope – Infectious Diseases in Context informationisbeautiful.net/visualizations… via Information is Beautiful

Fantastic keynote talk at #biodata18 by Steven Salzberg 💙💛 from Johns Hopkins University on adventures and misadventures in genome data mining with lots of fun stories about horizontal gene transfer. #blastology #hgt #genomics #datamining

KrakenUniq (formerly KrakenHLL): confident and fast metagenomics classification using unique k -mer counts genomebiology.biomedcentral.com/articles/10.11… github.com/fbreitwieser/k…

We've released another Kraken (KrakenUniq, just published) Very elegant work by Florian Breitwieser using randomized counting algorithm to enhance the Kraken metagenomics software. #microbiome genomebiology.biomedcentral.com/articles/10.11…

If anyone needs a quick alignment coverage calculation + visualization on the terminal, the tool `bamcov` is now available at github.com/fbreitwieser/b…

Real-time measurement of protein–protein interactions at single-molecule resolution using a biological nanopore: nature.com/articles/nbt.4…

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/

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/bioinformatics…

Have been looking forward to this paper from Daehwan Kim and Steven Salzberg 💙💛 biorxiv.org/content/biorxi… FM index based metagenomic classificn

With so much talk of corp tax cuts, thought it was interesting that median effective tax rate for $spx is near a record low Ned Davis Research

Who is interested in SVs, human genomics/clinical data, Texas, can program and has a PhD? Lets work together! Apply: fritzsedlazeck.github.io

I submitted NGMLR + Sniffles preprint to a bioinformatics peer price. Illustrating an advance long read mapping and SVs calling using @Pacbio / Oxford Nanopore and probes systematic errors in short read SV calling. Please vote + RT: thinkable.org/submission_ent… Philipp Rescheneder Michael Schatz

Removing Contaminants from Metagenomic Databases biorxiv.org/content/early/… clean genomes: ccb.jhu.edu/data/eupathDB/

KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts from Florian Breitwieser and Steven Salzberg 💙💛 biorxiv.org/content/early/… code github.com/fbreitwieser/k… cc Krista Ternus @brooksph Titus Brown Todd J Treangen

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/…

New paper in press today at Nature Reviews Genetics: 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

Krista Ternus Florian Breitwieser Steven Salzberg 💙💛 @brooksph Titus Brown Todd J Treangen 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!

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 Cole Knaflic