BOL

github.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...

rrwick.github.io - Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...

academic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...

gfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...

github.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...

journals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAP

github.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...

rstudio.github.io - Leaflet is one of the most popular open-source JavaScript libraries for interactive maps. Features Interactive panning/zooming Compose maps using arbitrary combinations of: Map...

paleogenomics.irmacs.sfu.ca - This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes. Download Program, version 1.01 (July 10, 2012, documentation updated in August 2014) Examples...

bioinformaticsworkbook.org - Genetic map, as the name suggest is simply knowing the relative positions of specific sequences across the genome. There are various methods to generate them, but most popular method is to use a cross between the known parents and examining their...