perl-for-reysenbach-lab
These are perl scripts I developed over many years as a Bioinformaticist for the Reysenbach Lab at PSU. The Reysenbach Lab studies microbial diversity in extreme environments. Lotta fasta utilities here if you are into that sort of thing. (by jmeneghin)
faster-perl-for-reysenbach
Tracks the progress of making old Perl scripts faster and more maintainable. Working from Meneghin's perl-for-reysenbach-lab repository of bioinformatics scripts. (by duffee)
| perl-for-reysenbach-lab | faster-perl-for-reysenbach | |
|---|---|---|
| 3 | 1 | |
| 3 | 0 | |
| - | - | |
| 10.0 | 3.9 | |
| over 1 year ago | 5 months ago | |
| Perl | Perl | |
| - | - |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
perl-for-reysenbach-lab
Posts with mentions or reviews of perl-for-reysenbach-lab.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2024-03-15.
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Faster tetranucleotide (k-mer) frequencies!
I saw Jennifer's post about re-writing her perl scripts in python and how she saw a 2.5 times improvement.
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Calculating tetranucleotide (k-mer) frequencies
In 2016 I wrote a Perl script for the Reysenbach lab that calculates k-mer frequencies, for all k-mers in a given sequence. It was made public soon after, and you can find get_kmer_frequencies.pl on my Github page.
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Get GC Content
I wrote a Perl script that calculates GC content for all the sequences in a fasta file back in 2010 for the Reysenbach Lab, and it was made publicly available soon after. You can find get_gc_content.pl on GitHub (https://github.com/jmeneghin/perl-for-reysenbach-lab)
faster-perl-for-reysenbach
Posts with mentions or reviews of faster-perl-for-reysenbach.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2024-03-15.
-
Faster tetranucleotide (k-mer) frequencies!
I have an interest in Perl and Science, so time to roll up sleeves and learn me some profiling/benchmarking. What follows is my internal monologue and the notes I scribbled down during the learning process. For those that want to follow along, I've created a small repo.
What are some alternatives?
When comparing perl-for-reysenbach-lab and faster-perl-for-reysenbach you can also consider the following projects:
hyperfine - A command-line benchmarking tool
dotfiles - is it worth the time?