GAM-NGS: genomic assemblies merger for next generation sequencing
GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best...Tags: GAM-NGS, Genomic, Assemblies, Merger, Sequencing, NGS
2505 days ago
S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can be efficiently compared. The tool includes funct...Tags: S-plot2, Rapid, Visual, Statistical, Analysis, Genomic, Sequences
2004 days ago
GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documen...Tags: GRAbB, Selective, Assembly, Genomic, Regions, New, Niche, Genomic, Research
1888 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn gra...Tags: GRIDSS, Genomic, Rearrangement, IDentification, Software, Suite
1411 days ago
Genomic Open-source Breeding informatics initiative
To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs. To transform breeding by connecting diverse data with precision breeding tools to advance yields and adaptation to loc...Tags: Genomic, Open-source, Breeding, informatics, initiative
1177 days ago
BEDOPS v2.4.26: high-performance genomic feature operations
BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic...Tags: BEDOPS, high-performance, genomic, feature, operations, NGS, BED
2481 days ago
Web Apollo: a web-based genomic annotation editing platform
Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to desc...Tags: Web, Apollo, genomic, annotation, editing, platform
2436 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in ...Tags: Taxoblast, pipeline, identify, contamination, genomic, sequence
2317 days ago
SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.Tags: SVfinder, Tool, detecting, genomic, rearrangement, DNA-seq
2296 days ago
kraken: A universal genomic coordinate translator for comparative genomics
If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomicsTags: kraken, universal, genomic, coordinate, translator, comparative, genomics
2304 days ago