CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library...2372 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 current SP...2372 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 using Hi-C yie...2372 days ago
HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be...2352 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate al...2366 days ago
ECTOOLS: Long Read Correction and other Correction tools
Long Read Correction and other Correction tools This package is a loose collection of scripts. To run the correctionroutine see the section below. Descriptions of the other scriptsa...2364 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of th...1619 days ago
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://ge...2331 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig...2310 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 demo2310 days ago