Ra assembler - a de novo DNA assembler for third generation sequencing data
Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Facult...lectrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome In...2379 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation o...ntegrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the gr...bsp;From de Bruijn Graphs to Rectangle Graphs for Genome As...2379 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 us...2379 days ago
GPOPSIM: a simulation tool for whole-genome genetic data
GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter...2359 days ago
JPred4: A Protein Secondary Structure Prediction Server
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.2377 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool eva...Reading a pre-existing reference genome from one or more FASTA files...., generating an artificial reference genome based on input parameters (le...te. Applying alignment tools to the genome an...2373 days ago
LRCstats: Long Read Correction Statistics
LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted...uncorrected long reads (uLR) and the corresponding sequences in the reference genome (R...2371 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the imple...s (embl format) can be automatically loaded into the freely available Artemis genome vi...2368 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome in...2366 days ago
AliTV—interactive visualization of whole genome comparisons
AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annota...2366 days ago