Results for "Genomes"
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Digest: In silico restriction digest of complete genomes
This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated. A tool for restriction digest of longuser's sequences...Tags: Digest, In silico, restriction, digest, complete, genomes
2177 days ago
- CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Ass...
Tags: CheckM, Assessing, quality, microbial, genomes, recovered, isolates, single, cells, metagenomes, Validation
2167 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropr...Tags: GenomeMapper, Simultaneous, alignment, short, reads, multiple, genomes
2165 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to imp...Tags: Ranbow, haplotype, assembler, polyploid, genomes, Assembly, NGS
2158 days ago
mmgenome: Tools for extracting individual genomes from metagneomes
The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reprod...Tags: mmgenome, Tools, extracting, individual, genomes, metagneomes
2089 days ago
- GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environ...
Tags: GTDB-Tk, toolkit, assign, objective, taxonomic, classifications, bacterial, archaeal, genomes
2077 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use revers...Tags: BASE, practical, de novo, assembler, large, genomes, long, NGS, reads
2018 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line. CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that are c...Tags: CSBFinder, Discovery, colinear, syntenic, blocks, prokaryotic, genomes
2013 days ago
ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC,...Tags: ALLHiC, Phasing, scaffolding, polyploid, genomes, Hi-C, data, assembly
1956 days ago
