MLST with colorid
I am pleasantly surprised by how well ColorID works with MLST. For some background, please see my previous post on cgMLST.
Posts by Category
- MLST 2
- perl 2
- conferences 2
- bioinformatics 2
- travel 2
- hash 2
- mlst 2
- genbank 1
- CV 1
- jekyll 1
- update 1
- linux 1
- wgMLST 1
- cgMLST 1
- EToKi 1
- ChewBBACA 1
- ColorID 1
- memories 1
- flag 1
- datasets 1
- tabs 1
- github 1
- rust 1
- colorid 1
- BioNumerics 1
- genomic-epidemiology 1
- open-source 1
- file-conversion 1
- VCF 1
- MSA 1
- fasta 1
- distances 1
- distance-matrix 1
- experiment 1
MLST
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...
perl
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.
conferences
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...
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...
bioinformatics
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...
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...
travel
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...
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...
hash
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...
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...
mlst
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...
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...
genbank
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...
CV
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...
jekyll
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...
update
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...
linux
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 ...
wgMLST
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...
cgMLST
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...
EToKi
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...
ChewBBACA
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...
ColorID
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...
memories
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 ...
flag
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 ...
datasets
Benchmark datasets
Over the last several years, we have been generating benchmark datasets.
tabs
We can make this beautiful and searchable
You might have seen this message on GitHub for a tab separated file.
github
We can make this beautiful and searchable
You might have seen this message on GitHub for a tab separated file.
rust
MLST with colorid
I am pleasantly surprised by how well ColorID works with MLST. For some background, please see my previous post on cgMLST.
colorid
MLST with colorid
I am pleasantly surprised by how well ColorID works with MLST. For some background, please see my previous post on cgMLST.
BioNumerics
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...
genomic-epidemiology
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...
open-source
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...
file-conversion
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 ...
VCF
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 ...
MSA
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 ...
fasta
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 ...
distances
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 ...
distance-matrix
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 ...
experiment
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...