Results for "Simulation"

Tags

  • WgSim

    Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors...

    Tags: Bioinformatics, NGS, Reads, Silulator, INDEL, SNPs, Simulation

    2835 days ago

  • Nemo – A stochastic, individual-base, genetically explicit simulation platform

    A recombination map has been added for all multi-locus traits. The map positions (chromosomal) for neutral markers (e.g. SNPs) and loci under selection (QTLs, deleterious mutations, DMIs) can now be specified explicitly, or set at random. The map can hold an unlimited number of loci...

    Tags: Bioinformatics, Nemo, Simulation, Chromosome, Genome, NGS

    2735 days ago

  • WGS Celera Assembler version 8.3rc2

    These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.This distribution package provides a stable, tested, documented version of the software.  The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distri...

    Tags: Bioinformatics, wgs-assembler, WGS, PBcR, Pacbio, Correct, Packages, Tools, Simulation, Fastq

    2544 days ago

  • simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data

    simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be pres...

    Tags: simNGS, simLibrary, Software, Simulating, Next-Gen, Sequencing, Simulation

    2312 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

  • jobTree based python wrapper to run the genome simulation tool suite Evolver

    evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also...

    Tags: jobTree, python, wrapper, genome, simulation, tool, suite, Evolver

    2302 days ago

  • GPOPSIM: a simulation tool for whole-genome genetic data

    GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with ...

    Tags: GPOPSIM, simulation, tool, whole-genome, genetic, data

    2262 days ago

  • sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)

    Required python modules biopython intervaltree numpy scipy tqdm PyYAML

    Tags: sim3C, Read-pair, simulation, 3C-based, sequencing, methodologies, HiC, Meta3C, DNase-HiC

    1962 days ago

  • ALF--a simulation framework for genome evolution.

    Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article: Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimo...

    Tags: ALF, simulation, framework, genome, evolution

    1618 days ago