Results for "ploidy"
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InfoGenomeR: Integrative reconstruction of cancer genome karyotypes
...n that uses a breakpoint graph to model the connectivity among genomic segments at the genome-wide scale. InfoGenomeR integrates cancer purity and ploidy, total CNAs, allele-specific...1100 days ago
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold...encing coverage is available, or the true contig ploidy is low. https://github...2631 days ago
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Genome Assembly Tools and Software - PART2 !!
...s produced by the Illumina Genome Analyzer ConPADE 1.00 – Contig Ploidy and Allele Dosage EstimationConPADE is a tool used to estimate contig ploidy and allele dosage in polyploi...2689 days ago
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List of Bioinformatics Software Tools for Next Generation Sequencing
...space- separated format, VCF, pileup, HGVS Output: VCF, JSON, Statistics ABSOLUTE Description: (Broad Institute); can estimate purity and ploidy to compute absolute copy numb...2913 days ago
Frequent parameters for bioinformatics tools !
...; samtools mpileup (SNP detection) -uRI bcftools call (SNP detection) --variants-only --skip-variants indels --output-type v --ploidy 1 -c SNPsift filter...1289 days ago
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Bio-Scripts
- ...(BETA Tool) Denoises read counts to produce denoised copy ratios DetermineGermlineContigPloidy (BETA Tool) Determines the baseline contig ploidy for germline samples given co...
2079 days ago
Corona variant calling steps !
...bam bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref_genome/sequences.fasta results/bam/$basename.sorted.bam bcftools call --ploidy 1 -m -v -o results/bcf/$basen...1049 days ago
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nQuire: a statistical framework for ploidy estimation using next generation sequencing
nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemente...Tags: nQuire, statistical, framework, ploidy, estimation, next, generation, sequencing, NGS
2044 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on...Tags: statistical, framework, ploidy, estimation, NGS, short-read, data
1925 days ago
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Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...quo; is part of the final assembly? What do you think contamination would look like in the kmer plot? What can the kmer graph tell you about the ploidy of the organism?...1341 days ago
