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...2377 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...2357 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool eval...: Reading a pre-existing reference genome from one or more FASTA files....y, generating an artificial reference genome based on input parameters (le...ate. Applying alignment tools to the genome...2371 days ago
LRCstats: Long Read Correction Statistics
LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted b...uncorrected long reads (uLR) and the corresponding sequences in the reference genome...2369 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 implem...ns (embl format) can be automatically loaded into the freely available Artemis genome...2367 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...2364 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 annot...2364 days ago
Dot, an interactive viewer for genome-genome comparison
Dot, an interactive dot plot viewer that allows genome scientists to visualize genome-genome alignments in order to evaluate new...commonly used software method for aligning genome assemblies. A quick script ca...on demand. Dot, an interactive viewer for genome-...2360 days ago
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PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Ser...onservative levels, and genetic variation from pan-genome sight. At the same time, anal...al result data from many other programs, including genome...2351 days ago