repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into...repeats. The previous standard for evaluation (Hunt et al., Genome Biology,...2279 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.2206 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Ci...s using long sequencing reads", Hunt et al, Genome Biology...2224 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to...amples of the various output types, see the CGView gallery. http://wishart.biology....2188 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotid...ssification using targeted short read sequencing.” Source Code for Biology...2138 days ago
2074 days ago
Biotite: A general framework for computational biology
The package is open source and freely available at GitHub (https://github.com/biotite-dev/biotite). This package is.... The Biotite package bundles popular tasks in computational biology...2008 days ago
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EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combin...from whole-exome sequencing data.EXCAVATOR has been published on Genome Biology (http://genomebiology....1990 days ago
Osprey: Network Visualization System
Osprey is a software platform for the visualization of complex biological interaction networks. Osprey buil...Stark, C., Tyers M. "Osprey: A Network Visualization System." Genome Biology 2003 4(3):R22 [Genome Biology]...1974 days ago