Results for "Genome"
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Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by charact...Tags: Flanker, Python, mobile, genetic, elements, HGT, genome, genes
1156 days ago
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
1149 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
1090 days ago
- HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be define...
Tags: HapSolo, optimization, approach, removing, secondary, haplotigs, diploid, genome, assembly, scaffolding
1086 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
1041 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
1037 days ago
- What is a k-mer anyway? A k-mer is just a sequence of k characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get all k-mers from a sequence you need to get the first k characters, then move just ...
Tags: k-mer, counting, learn, teach, skill, genome, reads
985 days ago
- Lab focus on understanding how organisms adapt to their environments. They combine omics approaches with detailed molecular and phenotypic analyses to get a comprehensive picture of adaptation. Our aim at being internationally recognized as a leading lab in the field of environmental adaptation. ...
Tags: adaptation, genome, fly, repeats, transposable, elements
984 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
961 days ago
