Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not inc...aphs that miniasm makes. That's where Minipolish comes in. With a single comma...1616 days ago
modelStudio: a package automates the explanation of machine learning predictive models
The modelStudio package automates the explanation of machine learning predic...ch effort. Break down your model and look into its ingredients with only a few lines of code.1565 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher...1564 days ago
Leaflet: JavaScript libraries for interactive maps
Leaflet is one of the most popular open-source JavaScript libraries for interacti...Compose maps using arbitrary combinations of: Map tiles Markers Polygons Lines Popups GeoJSON Create...1547 days ago
BlobToolKit: A toolkit for genome assembly QC
Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-ba...genomic datasets even for highly fragmented assemblies. BlobTools2 is a comma...1536 days ago
Juicebox: Visualization and analysis software for Hi-C data
Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juic...s available on the wiki. Instructions below pertain primarily to usage of comma...1536 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 h...ed and indel reads, although this can be customized to any set of reads at the comma...1518 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' genom...1505 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/1452 days ago
wgd—simple command line tools for the analysis of ancient whole-genome duplications
wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis...1383 days ago