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Variant simulation software tools | Whole-genome sequencing data analysis

Various methods dealing with the comparison, annotation, visualization and especially the detection of structural variations (SVs) were published (Lam et al., 2010; Nielsen et al., 2010; Xi et al., 2010). The simulation of SVs is a powerful, quick…
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DWGSIM
Desktop

DWGSIM

Whole genome simulator for next-generation sequencing. DWGSIM generates base…

Whole genome simulator for next-generation sequencing. DWGSIM generates base error qualities based on a parametric model.

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BAMSurgeon
Desktop

BAMSurgeon

Tools for adding mutations to .bam files, used for testing mutation callers.…

Tools for adding mutations to .bam files, used for testing mutation callers. One of the primary use cases for BAMSurgeon is to test somatic mutation calling methods.

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RSVSim
Desktop

RSVSim

Simulates deletions, insertions, inversion, tandem-duplications and…

Simulates deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed…

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pIRS
Desktop

pIRS profile based Illumina pair-end Reads Simulator

It is developed for de novo data simulation. pIRS uses empirical distribution…

It is developed for de novo data simulation. pIRS uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and…

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tHapMix
Desktop

tHapMix simulating Tumour samples through Haplotype Mixtures

Enables the creation of tumour samples with different ploidy, purity and…

Enables the creation of tumour samples with different ploidy, purity and polyclonality features. tHapMix easily scales to simulation of hundreds of somatic genomes, while re-use of real read data…

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Bamgineer
Desktop

Bamgineer

Introduces user-defined haplotype-phased allele-specific copy number events…

Introduces user-defined haplotype-phased allele-specific copy number events into an existing BAM file with a focus on targeted and exome sequencing experiments. Bamgineer can be used to add or delete…

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IntSIM
Desktop

IntSIM

An integrated simulation system to simulate common DNA variants and to generate…

An integrated simulation system to simulate common DNA variants and to generate sequencing reads for mixture genomes. IntSIM has three novel features in comparison with other simulation programs: (1)…

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VarSim
Desktop

VarSim

A framework for assessing alignment and variant calling accuracy in…

A framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it…

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SMaSH
Desktop

SMaSH

A benchmarking methodology for evaluating germline variant calling algorithms.…

A benchmarking methodology for evaluating germline variant calling algorithms. Authors generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes…

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SCNVSim
Desktop

SCNVSim

A tool for simulating somatic CNVs and structure variations SVs. Other than…

A tool for simulating somatic CNVs and structure variations SVs. Other than multiple types of SV and CNV events, the tool is capable of simulating important features related to tumor samples…

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srv
Desktop

srv Simulator of Rare Variants

Simulates large populations of gene sequences using a forward-time simulation…

Simulates large populations of gene sequences using a forward-time simulation approach. srv is capable of simulating several multi-locus fitness schemes with arbitrary diploid single-locus selection…

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GenomeSmasher
Desktop

GenomeSmasher

A set of tools used to create diploid fasta files with containing SNPs, indels,…

A set of tools used to create diploid fasta files with containing SNPs, indels, duplications, deletions, and translocations. These FASTA files can then be used in conjunction with next-generation…

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SInC
Desktop

SInC Snp, Indel and Cnv

An open-source variant simulator and read generator capable of simulating all…

An open-source variant simulator and read generator capable of simulating all the three common types of biological variants taking into account a distribution of base quality score from a most…

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msbar
Desktop

msbar

Mutates a sequence. msbar is an Emboss package that changes a sequence,…

Mutates a sequence. msbar is an Emboss package that changes a sequence, attempting to emulate various forms of mutation. It reads one or more sequences and writes an output file with a set of…

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MySSP
Desktop

MySSP

Constructs an initial DNA sequence at the root of the tree and simulates…

Constructs an initial DNA sequence at the root of the tree and simulates evolution across the tree using a variety of common models of DNA evolution. MySSP is a program for the simulation of DNA…

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