Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but s...2257 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to...repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2249 days ago
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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work...ncing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X Genomic...2194 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 2015 Dec 29;16(1):294. doi: 1...2194 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the orig...Scaffolding of long read assemblies using long range contact information. BMC genomic...2163 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genome...amples of the various output types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.ht...2158 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-mod...ient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomic...2145 days ago
Epiviz: an interactive visualization tool for functional genomics data.
Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within g...2139 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), an...ssification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, 13. do...2108 days ago