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. The simulation of SVs is a powerful, quick and inexpensive approach to assess their performance and correctness.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Serves as a whole genome simulator for next-generation sequencing (NGS). DWGSIM is built on WGSIM from SAMtools and can deal with ABI SOLiD and Ion Torrent data and execute various assumptions about aligners and positions of indels. This software produces base error qualities based on a parametric model. It can also simulate reads and evaluate mappings.
Simulates Illumina reads using empirical profiles. pIRS is a simulator developed to reproduce similar to those generated from the Illumina platform. This method be helpful for developing next-generation sequencing (NGS) software such as de novo assembly, single-nucleotide polymorphism (SNP) calling and structural variation detection. This application can also be useful for applications that need heterozygous data.
Adds mutations to .bam files. BAMSurgeon allows creation of synthetic mutations for generating somatic structural variants (SVs). The software can create SVs through read selection, local sequence assembly, manipulation of assembled contigs, and simulation of sequence coverage over the altered contigs. It was used to generate synthetic tumour-normal pairs, with the same set of target mutations, that differ by the division of reads into tumour and normal sequence sets, aligner or cell line.
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 synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic genomes biologically relevant. VarSim simulates and validates a wide range of variants, including single nucleotide variants, small indels and large structural variants. It is an automated, comprehensive compute framework supporting parallel computation and multiple read simulators.
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 haplotype-phased and allele-specific copy number events to existing alignments of targeted next-generation sequencing (NGS) data. It aids in development and benchmarking of copy number variation (CNV) calling and other sequence data analysis tools and pipelines.
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 uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.