Search Results for "mer"
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Showing 21 open source projects for "mer"
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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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GeneMiner2 is a comprehensive toolkit designed for phylogenomic genomics. Its main functionalities include: - Mining single-copy nuclear genes, plastid genes/genomes, and other molecular markers from next-generation sequencing data. - Aligning and trimming multiple molecular markers, constructing concatenated and coalescent-based phylogenetic trees, and calibrating tree time. Reference for GeneMiner2: Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y. 2026. GeneMiner2:...
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PLEK
predictor of long non-coding RNAs and mRNAs based on k-mer scheme
INSTALLATION Pre-requisite: 1. Linux 2. C/C++ compiler (i.e. gcc, g++) 3. Python 2.5.0 or later versions (http://www.python.org/) Steps: 1. Download PLEK.1.2.tar.gz from https://sourceforge.net/projects/plek/files/ and decompress it. $ tar zvxf PLEK.1.2.tar.gz 2. Compile PLEK. $ cd PLEK.1.2 $ python PLEK_setup.py USAGE python PLEK.py -fasta fasta_file -out output_file -thread number_of_threads -minlength min_length_of_sequence -isoutmsg 0_or_1... -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. ... -
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EDCC-CNG
Exploration and categorization of CREs and CRMs
...CNG provides an unbiased neural network approach to assess the importance of positional features that were determined by EDCC. To sustain a high computational performance even for large datasets, the mostly in Python 3 written programs use k-mer based indexing, parallelization and a neural network approach for categorization. For further information please refer to the publication: doi.org/10.1371/journal.pone.0190421 -
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CoSA (Concurrent Subtractive assembly) is a package to detect differential short sequencing reads by comparing two groups of metagenomes on the basis of kmer frequencies. KMC 2 is one of the fastest k-mer counting implementations, so we employ KMC 2 for k-mer counting in our package. Because in many cases we need to compare tens of or even hundreds of samples, we adopt the concurrent hash table in Libcuckoo for efficient k-mer counting. Once the differential reads are extracted, they can be used for downstream analysis including assembly to identify genes that are differentially abundant between groups of metagenomes (e.g., healthy vs diseased). ...
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PB-sQF_BacterialTyping
Bacterial Typing from either assembled or raw short reads file
Probability Binning - signature Quadratic Form, PB-sQF, types unknown sequence to one of the 628 bacterial library genomes which gives the smallest test statistics thus most similar library strain. The input file is the k-mer counts of the unknown assembled genome sequence or raw short reads file in decimal format generated by KAnalyze developed by P. Audano et al. (https://sourceforge.net/projects/kanalyze/). The download included the library index, the library name and sample unknowns. -
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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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Subtractive Assembly
An approach for comparative metagenomics by assembling the differences
...Given two metagenomic datasets A and B, subtractive assembly approach first identifies reads that are likely sampled from abundant or unique genomes in A (or B vice versa), using Bloom-filter based k-mer counting. And one can assemble only these reads separately using metagenomic assemblers such as IDBA-UD. We further developed concurrent subtractive assembly (CoSA), which is an improved version of the subtractive assembly approach for detecting differential reads between two groups of metagenomes. Please check CoSA out at https://sourceforge.net/projects/concurrentsa/... -
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Maree
Marée des principaux ports de France
Horaire, hauteurs et coefficients des marées sur plus de 100 ports français et quelques ports en Grande Bretagne. Application entièrement autonome faite à partir des constantes harmoniques fournies par Previ Mer. Toutes les heures locales affichées, le sont en horaires d'été et d'hiver. Le menu permet de calculer les marées et d'en donner les spécificités sur une journée ou sur un mois au choix. Fixez votre propre seuil (hauteur mini pour pratiquer la navigation ou maxi permettant la pêche à pied). Lister les grandes marées d'une période choisie et éventuellement stocker les horaires des marées basses dans votre agenda Saisissez une hauteur d'eau et définissez pour quels horaires elle sera atteinte ou pour tel horaire saisi quelle hauteur d'eau. ... -
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NGSimple
NGS - Next-Generation Sequencing sIMulation PipeLinE
..../1.fastq/reads.fastq) from those designed libraries to assemblies. based on the parameters specified in CONFIG file. It will generate assmblies with different K-mer (./2.assembly/*), and choose the assembly with largest n50. Finally, it will produce a quartile summary and mummerplot for each for you to select a good parameter combination. insert_size.pl will take real Illumina data as -
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PriMux is a k-mer based library for genomic investigations, and for development of PCR signatures that may include degenerate base pairs
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K-mer counting
an efficient tools for k-mer acounting
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Quikr
Method for rapid reconstruction (phylotyping) of bacterial communities
Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that utilizes sparsity promoting ideas from the field of compressed sensing to reconstruct the composition of a bacterial community (when the input data is 454-like pyrosequencing data). This extremely fast method comes with a default training database but can be custom trained. Typically reconstruction is accurate down to the genus level. -
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HErCoOl
High-throughput Error Correction by Oligomers
Error correction software for next-generation sequencing data based on k-mer spectrum. -
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open-slx Weekly News
open-slx Weekly News
This project produces a weekly newsletter about Linux, Plasma Active, Mer and other mobile stuff. This Repository contains the Sources of the english and german Weekly News. The Sources are written in Docbook 4.5 -
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Database Modeller and Constructor, using the concept of MER, written in Java with the JGraph library. Initially developed for Unicamp Database discipline, offered by Ricardo Torres in 2007.1
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