Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of the Br...his workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3. Genome...1598 days ago
shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams
shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package. To create single-genome plot by aligning genome data...Single-genome plot menu. To cretae two-genome...1591 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 implement...very 25kb window (with some small overlap) for every region in the genome....1581 days ago
U-Plot: Genome U-Plot sample implementation
The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.1588 days ago
1584 days ago
JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wiki1574 days ago
Phytozome v12.1: plant science community hub for accessing palnts genomic data
Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the bro...alizing and analyzing JGI-sequenced plant genomes, as well as selected genomes...hytozome hosts 93 assembled and annotated genomes...1574 days ago
1571 days ago
tinycov: standalone command line utility written in python to plot coverage from a BAM file
Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome...1568 days ago
1523 days ago