Juicebox: Visualization and analysis software for Hi-C data
...box here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox j...1549 days ago
SvABA: Structural variation and indel detection by local assembly
...the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam&nb...1531 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 coverage plott...1518 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/PMC6733440/1465 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 workflows t...1396 days ago
1396 days ago
Caretta – A multiple protein structure alignment and feature extraction suite
...lies which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and addition...1248 days ago
1229 days ago
Pandoc: The universal markup converter
Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. Pandoc is a free and open-source document converter, widely used as a writing tool and as a basis for publishing workflows. More at https://pandoc.org/1216 days ago
Luigi: a Python package that helps you build complex pipelines of batch jobs.
...ge that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization, handling failures, command line integration, and much mo...1060 days ago