Results for "Assembly"
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Genome Assembly Tools and Software - PART2 !!
The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for your assembly. For the sake of computational me...Tags: Bioinformatics, Genome, Assembly, RNA, DNA, Sequence, NGS
2699 days ago
- MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms ...
Tags: Bioinformatics, Analysis, Assembly, Genome, MetaBAT, MetaGenomics, Contamination
2631 days ago
- PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable region of the 16S gene, or the constant regions aro...
Tags: Bioinformatics, Assembly, PANDASEQ, Genome, NGS, Illumina
2673 days ago
- Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome alignment and analysis Gingr - Interactive ...
Tags: Bioinformatics, Analysis, Assembly, Genome, Harvest, Alignment, Tools
2664 days ago
- The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links. Simple and interpretable. The purpose of the hi...
Tags: Bioinformatics, Analysis, Assembly, Genome, Visialization, Tool, View, Hive, Plot, HivePlot
2648 days ago
- ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is th...
Tags: Bioinformatics, Analysis, Assembly, Genome, ABACAS, Plot, View
2648 days ago
- BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:http://sourceforge.net/projects/brig If you have any questions or comments, post th...
Tags: Bioinformatics, Analysis, Assembly, Genome, BRIG, Plot, View, BLAST
2648 days ago
- Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count,&...
Tags: Bioinformatics, Analysis, Assembly, Genome, bedtools, View, Alignment, BAM, SAM
2641 days ago
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencin...Tags: Bioinformatics, Analysis, Assembly, Genome, ConPADE, Polyploidy
2641 days ago
