Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analysis, and the other is based on the Ks distribution map. Among them, Ks is defined as the average number of synonymous substitutions at each synonymous site, and there is also a Ka corresponding to it, which refers to the av...Tags: wgd, duplication, whole, genome, plan, tools, software, synteny, list
1160 days ago
InfoGenomeR: Integrative reconstruction of cancer genome karyotypes
InfoGenomeR is the Integrative Framework for Genome Reconstruction that uses a breakpoint graph to model the connectivity among genomic segments at the genome-wide scale. InfoGenomeR integrates cancer purity and ploidy, total CNAs, allele-specific CNAs, and haplotype information to identify the o...Tags: Integrative, reconstruction, cancer, genome, karyotypes, chromosome
1101 days ago
Tags: HapSolo, optimization, approach, removing, secondary, haplotigs, diploid, genome, assembly, scaffolding
1097 days ago
IVA: accurate de novo assembly of RNA virus genomes
IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all oth...Tags: iva, virus, assembly, genome, RNA
1052 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA a...Tags: Variant, Prokaryotic, virus, genome, snp, tutorial, galaxy
1048 days ago
Tags: k-mer, counting, learn, teach, skill, genome, reads
996 days ago
Tags: adaptation, genome, fly, repeats, transposable, elements
995 days ago
RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold mergingTags: RagTag, software, tools, scaffolding, improving, modern, genome, assemblies
972 days ago
GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules. I...Tags: GenomeTools, versatile, open, source, genome, analysis, software
828 days ago