User: Lee Katz

gravatar for Lee Katz
Lee Katz3.0k
Reputation:
2,960
Status:
Trusted
Location:
Atlanta, GA
Website:
https://about.me/lskatz
Twitter:
lskatz
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 6 days ago
Joined:
9 years, 4 months ago
Email:
l*****@gmail.com

I am a bioinformatics scientist at Centers for Disease Control and Prevention (CDC).  I am interested in evolution of bacterial pathogens including Vibrio and Listeria.  What I write here does not necessarily reflect the opinions or views of CDC.

Posts by Lee Katz

<prev • 369 results • page 1 of 37 • next >
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Blog: Micro Binfie Podcast
... We've recently launched a podcast on Microbial bioinformatics marrying computer science and microbiology. We share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast ...
bioinformatics binfie podcast microbial blog written 6 weeks ago by Lee Katz3.0k
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Comment: C: Mashtree tool for rapid WGS dendrograms
... It's just a newick format but images might still be a good idea. I'll think on it! ...
written 9 weeks ago by Lee Katz3.0k
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Tool: Mashtree tool for rapid WGS dendrograms
... Hi guys, I wanted to share with you my tool Mashtree. It uses Mash and QuickTree to rapidly make trees, so that you can rapidly estimate clusters of genomes. Let me know how it goes! https://github.com/lskatz/mashtree ...
tool quick perl dendrogram multithreaded tree written 9 weeks ago by Lee Katz3.0k
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Comment: C: Script To Calculate A Distance Matrix Based On Tree File
... This was amazingly fast, and my jaw dropped ...
written 21 months ago by Lee Katz3.0k
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Answer: A: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Here is the code that actually works after I did some digging. It's a little bit of a hack but I don't believe it will cause any problems. Also I changed it to `Bio::FeatureIO` which I think is a little more mainstream. In this one-liner, `###` is printed to the output file after each input featu ...
written 3.4 years ago by Lee Katz3.0k
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Answer: A: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Jean-Karim is correct that the GFF module will probably only output features. However, you probably can manually write to the file in your perl script! There is a method called `$obj->fh` which returns the filehandle of your GFF object. Therefore you could write to the file as desired. For ex ...
written 3.4 years ago by Lee Katz3.0k
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Answer: A: Pfge Prediction Based On Wgs
... I was looking for this answer yet again but didn't see anything yet again, curiously. Here is the script I've developed over time for anyone else who might be looking. https://github.com/lskatz/lskScripts/blob/master/pfgeOnGenome.pl Run with --help for usage. ...
written 3.4 years ago by Lee Katz3.0k
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Comment: C: Portable genome browser
... I appreciate the idea @Jean, but @genomax2 is right that I would like to send something interactive over email. I can package and prepare something, but it needs to be ready to go when the recipient opens it from email. ...
written 3.4 years ago by Lee Katz3.0k
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Comment: C: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Could you write an example of what you'd like to see in the GFF3 file? ...
written 3.4 years ago by Lee Katz3.0k
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Comment: C: Portable genome browser
... Unfortunately, running this and probably any other JS-based browser locally will trigger cross-site errors, as I have learned from Genoverse this morning. I thought that a JS-based client would be the optimal solution; however, there is a fundamental security obstacle. ...
written 3.4 years ago by Lee Katz3.0k

Latest awards to Lee Katz

Popular Question 9 months ago, created a question with more than 1,000 views. For Polytomies and tree comparison
Great Question 9 months ago, created a question with more than 5,000 views. For Bio-Javascript?
Popular Question 9 months ago, created a question with more than 1,000 views. For Bio-Javascript?
Great Question 9 months ago, created a question with more than 5,000 views. For bcftools merge; retaining sample names
Great Question 9 months ago, created a question with more than 5,000 views. For Illumina Assembly Gap Closure
Scholar 10 months ago, created an answer that has been accepted. For A: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
Popular Question 17 months ago, created a question with more than 1,000 views. For bcftools merge; retaining sample names
Popular Question 17 months ago, created a question with more than 1,000 views. For Add soft clipping to a bam file
Popular Question 17 months ago, created a question with more than 1,000 views. For Paired End Vs Single End Detection
Popular Question 17 months ago, created a question with more than 1,000 views. For Bio-Javascript?
Popular Question 20 months ago, created a question with more than 1,000 views. For Add soft clipping to a bam file
Great Question 20 months ago, created a question with more than 5,000 views. For bcftools merge; retaining sample names
Popular Question 20 months ago, created a question with more than 1,000 views. For bcftools merge; retaining sample names
Popular Question 20 months ago, created a question with more than 1,000 views. For Paired End Vs Single End Detection
Great Question 20 months ago, created a question with more than 5,000 views. For Bio-Javascript?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Reverse Complement A Genbank File
Popular Question 20 months ago, created a question with more than 1,000 views. For Bio-Javascript?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How To Translate Old Parameters In New Version Of Blast 2.2.27 +
Popular Question 20 months ago, created a question with more than 1,000 views. For EC number regular expression
Popular Question 20 months ago, created a question with more than 1,000 views. For Outgroup from command line
Popular Question 21 months ago, created a question with more than 1,000 views. For Bio-Javascript?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Add soft clipping to a bam file
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bio-Javascript?
Great Question 2.4 years ago, created a question with more than 5,000 views. For Bio-Javascript?
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: How Much Does It Cost To Align A Flowcell In The Cloud?

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