Results for "Assembly"
Tags
GARM:Genome Assembly, Reconciliation and Merging
The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaf...Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, Merge, GARM
2741 days ago
GAM-NGS: genomic assemblies merger for next generation sequencing
GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus ...Tags: Bioinformatics, Analysis, Assembly, Genome, GAM-NGS
2741 days ago
- PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it ...
Tags: Bioinformatics, Analysis, Assembly, Genome, PEAR, Merge, Paired-End
2741 days ago
MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs) Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any length in Multi-FASTA format to produce an improved c...Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, Merge, MeGAMerge
2741 days ago
- quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBi...
Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, QuickMerge
2741 days ago
- If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard to assemble using overlap-consensus-layout appr...
Tags: Bioinformatics, Analysis, Assembly, Genome, De Bruijn graph
2740 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
2664 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
2706 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
2698 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
2682 days ago
