Search Results for "mers"
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Showing 8 open source projects for "mers"
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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UniversalMer2
A CLI k-mer counting tool for multiple size of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). This kmax can be specified as any length or can be automatically determined by the longest repeated patterns found in the input sequence. -
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mers
Portable software and data related to Mersenne numbers
Portable software related to Mersenne numbers. Useful to automate certain tasks related to GIMPS (www.mersenne.org) for computers that cannot run the GIMPS software for whatever reason. Much of the code has been in use since 1990 or so by a few people. The project web site at https://mers.sourceforge.io/mersenne.html has data about Mersenne numbers from many people generated by this and other software, notably from the GIMPS project. -
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covid-chestxray-dataset
We are building an open database of COVID-19 cases with chest X-ray
To build a public open dataset of chest X-ray and CT images of patients who are positive or suspected of COVID-19 or other viral and bacterial pneumonia (MERS, SARS, and ARDS.). Data will be collected from public sources as well as through indirect collection from hospitals and physicians. All images and data will be released publicly in this GitHub repo. This project is approved by the University of Montreal's Ethics Committee #CERSES-20-058-D. We can extract images from publications. ... -
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HTSFinder
High-Throughput DNA Signature Finder
HTSFinder consists of three computational phases. This pipeline generates all the possibilities of k-mers for every genome individually and then determines their frequency in the entire database. Finally, DNA signatures of every species or strain are obtained in the database or multiple databases that have been involved in the pipeline. HTSFinder implements the parallel and distributed computational tool Hadoop for the second and third phases. -
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KAnalyze
DNA/RNA Sequence K-mer Toolkit
KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API. -
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RAMBO-K
Read Assignment Method Based On K-mers
RAMBO-K is a tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data. Please cite our publication (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137896) if you use RAMBO-K. We moved to GitLab, please visit our homepage for latest development. The latest stable versions of RAMBO-K will still be provided here. -
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Ferox
Ferox - Sequence Alignment with Fuzzy K-mers
Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file.
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