repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers t...e repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2279 days ago
MITObim - mitochondrial baiting and iterative mapping
This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full art...;454 and PacBio sequencing platforms. Below you can find a few basic t...2232 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct...tion, and more recent gene assembly (de-novo and genome-assisted) methods. The basic E...2232 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...2225 days ago
2217 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SO...SOAPaligner benefitted in time and space efficiency by a revolution in the basic d...2217 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular geno...xamples of the various output types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.ht...2189 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic a...2141 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),...assification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, 13. do...2139 days ago
CBS Comparative Microbial Genomics group - BioTools download page
he CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a cus...ed by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic D...2125 days ago