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...1111 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...2642 days ago
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...2700 days ago
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...2924 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...1300 days ago
2090 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...1060 days ago
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?...1352 days ago