Mugsy: multiple whole genome alignment tool
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and t...2351 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rectangle graph approach is already included into the&n...2331 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome...2331 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemen...nerating an artificial reference genome based on input parameters (length, repeat count, repeat...2326 days ago
mojolicious: a next generation web framework for the Perl programming language.
Back in the early days of the web, many people learned Perl because of a wonderful Pe...ful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session manageme...2316 days ago
2296 days ago
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
...accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython...2290 days ago
Generate interactive codon usage plots
Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demo2270 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon f...e performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on th...2264 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to j...from an adequate scaffolding evaluation are genome repeats. The previous standard for e...nome Biology, 2014) did not take into account repeats...2248 days ago