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., the recove...1867 days ago
HaploTypo: a variant-calling pipeline for phased genomes
...alling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers th...1598 days ago
1558 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA&n...1516 days ago
1458 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
...containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencin...1448 days ago
pggb: the pangenome graph builder
...line renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to...aph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity...1328 days ago
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
...al loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between population...1255 days ago
Applied Computational Genomics Course at UU: Spring 2020
...questions enabled by modern DNA sequencing technologies will be explored including sequence alignment, the identification of genetic variation, structural variation, and ChIP-seq and RNA-seq ana...1228 days ago
Collection of Graph Visualization tools !
...nce genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation and sequence are separated....465 days ago