Package: krepe
KREPEABOUT:Co-Authors Erika Pedersen and Aengus McGuinness created KREPE at a fellowship
with the Institute for Computing in Research.BACKGROUND INFORMATION:In bioinformatics, it's important to be able to use strands of DNA
to compare organisms, understand and assemble genomes, and get a better
picture of how everything works together in an organism. A common tool
is the k-mer(nucleotide sequences of length k). When a biologist is working
on figuring out a genome, or comparing a cat and a dog, they start with the
k-mers. The way they work is similar to a paper shredder; you put in a paper
(or multiple reads of the same sequence), and shred it into bits. Then, you
take all the paper bits and piece them back together in the same way as before,
by finding similarities in each of the pieces. This is useful to biologists
because sometimes there are errors when the machine reads a sequence, so with
multiple copies it's simple to find errors and toss them out early so they
don't affect the overall 'picture'.These k-mers are sometimes strung together to make stringy looking
graphs called 'De Bruijn Graphs', that are used to find a pathway through
a genome- this process of finding a pathway is called collapsing. 'Collapsing'
a De Bruijn graph is comparable to cobbling together different bus or train
routes that start at the place where the last one ends, and finding a way
to your destination.Another kind of graph that is useful is a bar graph. Bar graphs show the
appearances of k-mers and can be used to determine the quality of reads
and determine what type of organism is being seen.Dendrograms can be used to compare any number of organisms to each other
and see how genetically far apart they are. They have a vertical line from
the bottom left to the top right that demonstrates samples intersecting with
themselves, and the rest of the squares show intersections between different
samples. Venn diagrams are another way to demonstrate the overlap of organisms.Our program calculates Jaccard similarity (which is basically the amount that
things have overlapping, 1.00 being completely the same and 0.00 being completely dissimilar) and uses it for the dendrograms and the venn diagrams.DESCRIPTION:The goal of the project is to create a streamlined, easy to use
package and command line tool that allows users to count k-mers
and easily generates the following:A list of the occurring k-mers in the given file that occur more
than onceA bar graph that shows the frequency of said k-mer occurrenceA De Bruijn graph that can then be used for genome assemblyA dendrogram that models genetic similarity and metadataA Venn Diagram that models genetic similarityThe package is protected by copyright under the GNU General Public
LicenseINSTALLATION:Use the package manager [pip]
(https://pip.pypa.io/en/stable/) to install krepe$pipinstallkrepeOR you can install without pip by using git:$gitclonehttps://github.com/RGBwalnut/Kmer-Counting-AnalysisUSAGE:The inputs that are allowed are .fasta, .fastq, and .fna.ROADMAP:This package is completely open-sourced and is being updated by
authors Erika Pedersen and Aengus McGuinness as needs ariseCONTRIBUTING:Contributions will be accepted, in the instance that the contributor
is willing to conform with the following:A. be listed as a minor contributor in the descriptionB. not be listed under the copyrightC. be willing to hear suggestions on minor changes to the proposed
contributionAs well as in the instance the authors deem the
contribution useful.