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Posts
Erdos Bacon number
Some friends were joking around online about their Kevin Bacon number. “I bumped into an actor one time who worked with Kevin Bacon.” “I went to high school ...
Adapter trimming
After sequencing, one of the first steps is to remove adapter sequences. These are most commonly the sequences that are either used to initiate sequencing li...
Pixi basics Permalink
I wrote a post on the microbifie blog on how to get started with Pixi.
Call for action: bioinformatics conferences
Every fiscal year, we have to predict where we are going to travel over the whole next year. However, conferences mainly post on their own website, making no...
Hash collision experiment
I have talked a bit about hashes with MLST but one crucial issue with hashes is whether they have collisions. In other words, if we have two sequences, there...
What does it take to switch over to BAM from FASTQ? Permalink
I wrote a post on the microbifie blog.
Hash MLST analysis
With EToKi and perhaps future MLST callers, we are possibly looking at a new class of MLST databases 1. I’m not sure which caller was actuall...
List of bioinformatics conferences
Every fiscal year, we have to predict where we are going to travel over the whole next year. However, conferences mainly post on their own website, making no...
Converting a set of VCFs to distances
I think that converting a bunch of VCF files to an alignment is still an artisinal thing. I made this sort of task in the Lyve-SET pipeline back in 2013 and ...
Open source alternatives
BioNumerics is sunsetting in December 2024. This is an issue especially in the PulseNet community where the network relies on this software to do many things...
MLST with colorid
I am pleasantly surprised by how well ColorID works with MLST. For some background, please see my previous post on cgMLST.
We can make this beautiful and searchable
You might have seen this message on GitHub for a tab separated file.
Benchmark datasets
Over the last several years, we have been generating benchmark datasets.
The memories
I was cleaning out my office and found a flag that was given to me a few years ago. The legendary Peter Gerner-Smidt had become a citizen and had given some ...
How to call whole genome MLST on the command line
I have been asked in many different contexts how to call alleles on the command line. In August 2022, I gave an internal workshop on how to call alleles on t...
How to be a good citizen on Linux
This is a short tutorial on how to be a good citizen in a shared Linux environment. At my own institution, there are many users per computer and we all have ...
mstdn.science
I am using my site to verify me on Mastodon. Nabil and Duncan spun up a Mastodon server at https://mstdn.science a few weeks ago and it has been wildly succe...
GenBank CV
I was inspired by Andrey Kislyuk’s post about 15 years ago on his personal website where he formatted his personal website to look like a GenBank file. I rec...
NFT of BRCA1
I’ve been sort of amazed ever since I heard about NFTs from Planet Money and now the New York Times. Basically you associate a place on the blockchain with ...
Downloading the breadth of SARS-CoV-2
I was trying to figure out how to download the breadth of all of SARS-CoV-2 genomes and so I started out with the two major repositories: NCBI and GISAID.
Minimizer perl module
I looked all over cpan but did not find a module to make Minimizers. Therefore I went ahead and made it in Bio::Minimizer.
Cluster detection using Mash
I have been racking my brain on what the command line version of a rapid cluster detection should be. As in, how can I rapidly figure out if two random geno...
Fixing the R package manager
R’s package manager is broken. I present to you my solution for it. $HOME is your home directory. 1) mkdir -pv $HOME/R/tmp 2) Edit $HOME/.Renviron and ad...
Mash perl module
Hey y’all, I made a new perl module to read and write Mash files. I made it a complete package, adding it to CPAN with documentation and adding unit testing...
Sampling the taxonomy database
I was a little frustrated that every time I wanted to try out my new Bio::DB::Taxonomy-based script, it would take a few minutes to run…. and then I would fi...
Custom Kraken database
Like many labs around the world, we use Kraken for contamination detection. This isn’t its intended purpose however because it is supposed to be a taxonomic...
Tree To Reads
It looks like Tree To Reads is online in a preliminary draft! I encourage everyone to try it out! http://biorxiv.org/content/early/2016/01/22/037655 Using...
Perl writing style
I’m taking a moment to reflect on a post that Torsten Seemann wrote a couple of years ago called “Minimum standards for bioinformatics command line tools.” ...
Krona snippet
I couldn’t find any kind of conversion Kraken and Krona recently and so I wrote up a little pipeline. Full script is available at lskScripts: https://github...
Edirect snippets
I have been really excited by the new-ish edirect utilities. I thought I’d put out my snippets and encourage anyone to show theirs too. I haven’t found a l...
The confusing vocabulary of public health and bioinformatics
In the very beginning of our Listeria project, we basically had an idea that we could use evolution to help in epidemiological investigations. The idea was ...
Blog posts
A few blog posts that I’ve really liked for my niche of public health and bioinformatics. I think one purpose of this blog can be to start gathering these p...
FASTQ must die! Long live SAM/BAM! (seconded!)
Here is a short rant but it becomes proactive. For those of you who don’t know me, I dislike having two fastq files per genome if they are paired end (PE). ...
personal
My thoughts
I’m not sure exactly what will go on this blog but I think I wanted some place to put my bioinformatics thoughts…
Welcome to Jekyll!
You’ll find this post in your _posts directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different wa...
old posts
I’ll see if I can continue my blog here. For previous entries, please see my blogspot at http://bioinformaticsthoughts.blogspot.com.
Site has been updated
Hey all, I updated the website to have a nicer interface. I also imported all my blogspot posts. Hopefully this will be a better online home for a long time.
Story about Ginger
Ginger passed away early this morning. Samantha had a good obituary for her
The war from Christmas
Today while I was raking leaves, my neighbor asked me if I was going to take my kids to the Pink Pig. This is a roller coaster that they set up at the mall a...
Finding liberty bells on vacation
I visited my brother in Philadelphia in February earlier this year and stopped by the Liberty Bell.
Golden Girls Murder Mystery
Samantha took me on a date yesterday to see the Golden Girls Murder Mystery.
Home Ownership
My wife and I have been furloughed from our jobs since October 1 and we aren’t sure when we’re going to be able to work. I want to be absolutely clear about ...
recipes
Moist flapjack with condensed milk
This recipe makes enough flapjack for two hungry children for several weeks of school lunches.
Chocolate Mousse
This recipe is from our friends the Poggios. We first ate it at their house and when they came to dinner we insisted they brought chocolate mousse with them.
A no-effort white loaf using a Kenwood Chef
This is how I make an easy and quick white loaf using my kitchen mixer. It’s trouble-free and reliable and a great time-saver.
Healthy Butter Chickpeas
This tastes so much like butter chicken.