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)
python-bioinformatics
Here are five of my bioinformatics scripts that have been converted from Perl to Python... Also a script for creating histograms of GC content. (by jmeneghin)
| perl-for-reysenbach-lab | python-bioinformatics | |
|---|---|---|
| 3 | 1 | |
| 3 | 0 | |
| - | - | |
| 10.0 | 0.0 | |
| over 1 year ago | about 2 years ago | |
| Perl | Python | |
| - | - |
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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)
python-bioinformatics
Posts with mentions or reviews of python-bioinformatics.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-01.
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Calculating tetranucleotide (k-mer) frequencies
This script is available for download on my GitHub page. To test for speed, I ran these two scripts five times each with two different sequence examples; a full genome file containing one long fasta record, and a Metagenome Assembled Genome (MAG) file containing 1708 shorter fasta records. Python was 2.9 times faster than Perl for the full genome, and 2.1 times faster than Perl for the MAG. I’ve recently become aware of the optimizing compiler RPerl, which allows Perl to be compiled into “ultra-fast and fully-compatible” C++, so I’m excited to try this out and see how the results compare to both Perl and Python.
What are some alternatives?
When comparing perl-for-reysenbach-lab and python-bioinformatics you can also consider the following projects:
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.