Serves for dissection of genome-wide allele-specific copy number in tumors. ASCAT infers ASCAT (accurate genome-wide allele-specific copy number) profiles from single nucleotide polymorphism (SNP) array data to evaluate and adjust both tumor cell aneuploidy and non-aberrant cell admixture. The ASCAT profiles generated can be useful for interpretation of cancer genome sequencing data and for identification of changes varying in size from point mutations to complex rearrangements.
Characterizes homeolog-specific polymorphisms (HSPs) in polyploid genomes. HANDS involves comparative alignments of next-generation sequencing (NGS) reads from polyploid and diploid progenitor-relatives onto a suitable reference sequence. It provides the ability to relate, on a genome-wide basis, specific homoallelic variants to particular agronomic traits. This tool increases the precision of crop-breeding solutions to address the challenge of global food security.
Allows users to perform genome wide association studies (GWAS) with biallelic single nucleotide polymorphisms (SNPs) in autopolyploids and diploids. GWASpoly is a R package that uses the Q (or P) + K method. The application aims to gather multiple models of gene action as well as investigate different types of kinship models for autopolyploids. It was tested with both simulated data and for a study involving a tetraploid potato diversity panel.
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 preserves noise and biases present in sequencing platforms. It is a versatile and scalable workflow for simulation of diverse tumour characteristics, such as polyclonality purity and aneuploidy.
Allows annotation of copy number changes in a fully automated fashion and quantification of copy number variations (CNV) heterogeneity between cells. AneuFinder quantifies aneuploidy in primary (tumour) cells in an unbiased and high throughput fashion. It is able to detect high-grade karyotype heterogeneity that would likely have been obscured using other platforms such as array comparative genomic hybridisation.
Achieves copy number variation (CNV) and aneuploidy detection from human or other large genomes. Wandy works through four steps: (i) BAM2BIN conversion; (ii) bin-filtering; (iii) bias-corrections; and (iv) quality-metrics summary. This application reports predicted chromosome regions with amplifications of deletions via LOG2 ratio.
Provides an approach for aneuploidies calling in single-cell RNA-sequencing. scploid is an R package performing for each cell, the identification of chromosomes including genes with potentially detected deviant expression, by applying a statistical method. It aims to supplies a straightforward and easy to interpret method for stem cell and embryonic research as well as assists users in determining genes possibly associated with copy number aberrations.