Results for "NGS"
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Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. Scarpa is ...Tags: Bioinformatics, Analysis, NGS, Scaffolding, Scarpa
2847 days ago
- Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common thread for the manual improvement of scaffolds. Desc...
Tags: Bioinformatics, Analysis, NGS, Scaffolding, WiseScaffolder
2847 days ago
- Microbiome analysis using a single application MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application. Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA Functional analysis using Int...
Tags: Bioinformatics, Analysis, NGS, Taxonomy, Functional Analysis
2835 days ago
- Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.Genome STRiP looks both across and within a set of sequenced...
Tags: Bioinformatics, Analysis, NGS, Genome STRiP, Genome, Variation
2792 days ago
- CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file...
Tags: Bioinformatics, Analysis, NGS, CrossMap, Genome, Coordinates
2793 days ago
- VALET is a pipeline for performing de novo validation of metagenomic assemblies. VALET checks a number of properties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance from each other in the assembly, the depth of coverage is fairly un...
Tags: Bioinformatics, Analysis, NGS, Valet, Genome
2776 days ago
- OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The application is especially optimized and adapted for the ...
Tags: Bioinformatics, Analysis, NGS, OrganellarGenomeDRAW, Draw, Genome, OGDRAW
2813 days ago
- RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from se...
Tags: Bioinformatics, Analysis, NGS, Repeats, TE, RepeatModeler, RECON, de-novo, family, Genome
2811 days ago
- We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the project name is "DmelChr4".
Tags: Bioinformatics, Analysis, NGS, TEs, TEannot, REPET, Pipeline, Repeats, Genome
2811 days ago
- Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files ...
Tags: Bioinformatics, Analysis, NGS, vcfR, R, Visualization, VCF, Genome
2810 days ago
