Results for "Analysis"
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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
2683 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
2683 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
2683 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
2683 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
2683 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
2682 days ago
- MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intend...
Tags: Bioinformatics, Analysis, NGS, Genome, Synteny, Homology, MCscan
2680 days ago
- Motif based sequence analysis suits The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. The MEME Suite supports motif-based analysis of DNA, RNA and protein s...
Tags: Bioinformatics, Analysis, Motif, Tools, Suite
2679 days ago
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include: Speed: Prodigal is an extremely fast gene r...Tags: Bioinformatics, Analysis, Gene, Prediction, Tool, Prodigal, Mathod
2673 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
2606 days ago
