Results for "Simulator"

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  • ART: Set of Simulation Tools

    ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user o...

    Tags: Bioinformatics, Stats, Reads, NGS, Simulator

    2702 days ago

  • MetaSim A Sequencing Simulator for Genomics and Metagenomics.

    Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes pr...

    Tags: MetaSim, Sequencing, Simulator, Genomics, Metagenomics

    2306 days ago

  • SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator

    SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios. SVEngine takes as input reference contigs in FASTA files, variant meta ...

    Tags: SVEngine, Allele, Haplotype, Aware, Structural, Variants, Simulator, Simulation

    1363 days ago

  • Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator

    Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets...

    Tags: Grinder, Biogrinder, Versatile, Omics, Shotgun, Amplicon, Sequencing, Read, simulator

    2500 days ago

  • NanoSim: nanopore sequence read simulator based on statistical characterization.

    NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and gen...

    Tags: NanoSim, nanopore, sequence, read, simulator, statistical, characterization

    2292 days ago

  • SimLoRD: A read simulator for third generation sequencing reads

    SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference can be read from a FASTA file or randomly gener...

    Tags: SimLoRD, read, simulator, third, generation, sequencing, reads, Pacific, Biosciences, SMRT, error, model

    2045 days ago

  • jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

    jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phyl...

    Tags: jackalope, swift, versatile, phylogenomic, high-throughput, sequencing, simulator, ngs

    1707 days ago

  • simuG: a general-purpose genome simulator

    Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Deletions, copy num...

    Tags: simuG, general-purpose, genome, simulator

    1582 days ago

  • mutatrix: a population genome simulator which generates simulated genomes.

    genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

    Tags: mutatrix, population, genome, simulator, generates, simulated, genomes, ngs, test

    1521 days ago