Results for "Variation and Disease"
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gSearch: a fast and flexible general search tool for whole-genome sequencing
gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.2112 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling...quencing data. NextSV integrates three aligners and three SV callers and generate...ily perform downstream annotation using ANNOVAR and disease gene discovery using Phenolyz...2112 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platfor...o trade-offs between accuracy and read length. Several studies require long and accurate reads including de n...e potential to achieve better and more accurate integration of...mong all competing algorithms and hig...2098 days ago
- ...all facets of modern genetics and bioinformatics research. Trans-disc...would lead to cures for human diseases; improvements to crop and livestock quality and yield;...es evolve to generate genetic variation in populations of organisms...effects on the patterning of variation within and between populati...
2082 days ago
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then...logy (SO), that can be currently assigned to each combination of an allele and a t...2078 days ago
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 use...athogens, artificial selection experiments, and for historical or ancient sam...are not preserved. It is implemented as a stand-alo...2053 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. Specifical...data to distinguish between diploids, triploids and tet...1934 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz.,...tion, the sensitivity of inferred TF-DNA binding strength, and num...1881 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes...tailored to resolve haplotypes in genetic variation analyses. HaploTypo inf...a phased reference genome. Availability and Implementation HaploTypo is implemented in Python 2.7 and Pyt...1612 days ago
- Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented...: nodes, which are labeled by sequences and ids edges, which connect two...hs, describe genomes, sequence alignments, and ann...
1572 days ago
