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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.
SInC / Snp, Indel and Cnv
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 commonly used next-generation sequencing instrument from Illumina. SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes.
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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 including aneuploidy, heterogeneity and purity. SCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterozygosity (LOH), and event break points, which is essential for developing and evaluating somatic CNV and SV detection methods in cancer genomics studies.
Simulates structural variation. Pysim-sv is a package for simulating high-throughput sequencing (HTS) data to evaluate performance of structural variation (SV) detection algorithms. Pysim-sv can introduce a wide spectrum of germline and somatic genomic variations, making simulated genomes more similar to real genomes. The package contains functionalities to simulate aneuploidy as well as heterogeneous tumor data, which is very useful in assessing performance of algorithms in tumor studies.
srv / Simulator of Rare Variants
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 models with random or locus-specific fitness effects. It uses realistic demographic and natural selection models estimated from empirical sequence data. The tool can be easily modified to reveal details of the evolutionary process or use alternative demographic or genetic models.
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 sequence evolution across a phylogenetic tree. It is designed for large-scale studies, including simulation of multiple replicates and outputs sequences into NEXUS, MEGA, or FASTA formats. MySSP has a fairly simple graphical user interface (GUI) for basic use, but also has a specialized batch script interpreter to allow for more complicated or large-scale simulations.
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