Search Results for "mer"
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Showing 32 open source projects for "mer"
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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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PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
...The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site. PWMScan takes as input a PWM, the background probabilities for the letters of the DNA alphabet, and a threshold score or a p-value. The search is carried out across the entire genome sequence. It can accept PWMs, such as those available in the Transfac or Jaspar databases as well as plain-text PWMs. ... -
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Meraculous-2D
Eukaryotic Genome Assembler
---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. ... -
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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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Suite of tools for DNA sequence analysis - searching (EST, mRNA, sequencer reads); aligning (ESTs, mRNA, whole genome); and analysis (repeats, kmers).
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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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COPEread
Connecting Overlapped Pair-End Reads
COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research. The full citation: COPE: An accurate k-mer based pair-end reads connection tool to facilitate genome assembly Binghang Liu; Jianying Yuan; Siu-Ming Yiu; Zhenyu Li; Yinlong Xie; Yanxiang Chen; Yujian Shi; Hao Zhang; Yingrui Li; Tak-Wah Lam; Ruibang Luo Bioinformatics (2012) 28(22): 2870-2874; doi: 10.1093/bioinformatics/bts563 -
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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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Trowel - Sequencing Error Corrector
Error Correction Module for Illumina Sequencing Reads
Trowel is an error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. This tool is the first tool that uses a quality threshold instead of a coverage cutoff in order to extract trusted k-mers. This tool guarantees high accuracy and speed. This tool has been developed since 21. Jan. 2013 by Euncheon Lim in Prof. Dr. Detlef Weigel's Lab in Max-Planck Institute for Developmental Biology. -
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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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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
...mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile). -
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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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mitoMaker
mitoMaker - a mitochondria pipeline wrapper script
...After various attempts to build different mitochondrial genomes in the lab I studied, a general pipeline started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a closely-related species, check it to see if all expected genomic features are present (since mitochondria is well conserved), check to see if the assembly might have circularized (since it's a circular DNA). If a feature was missing, or it hasn't circularized, try and assemble again with different assembler parameters (mainly k-mer). Rinse and repeat until the best build is found. -
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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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Musket - short read error corrector
a parallel short-read error corrector for Illumina sequencing
Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. -
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vtiger Norwegian Lang Pack
This is the Norwegian Localization for vtigerCRM
vTiger CRM på norsk! Se www.vtiger.no for mer informasjon. -
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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
