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High-throughput genomics has revolutionized biological re...ver, while the number of sequenced genomes grows by the day, quality...res for quantitative assessment of genome assembly, gene set, and tra...al candidates for large-scale phylogenomics studies, and the annotate...2974 days ago
- ...l is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read l...
2974 days ago
YASS :: genomic similarity search tool
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) se...en tries to extend them to local alignments. This genomic search tool uses multiple...seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simp...2982 days ago
- Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diplo...the following: Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Ok...A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozy...
2971 days ago
- ...evolutionary distance between closely related genomes. These distances can be us...d to rapidly infer phylogenies for big sets of genomes. Because andi does not com...at it scales even up to thousands of bacterial genomes. This readme covers all n...
2971 days ago
SATSUMA : Highly sensitive whole-genome synteny alignments.
Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and t...such as protein coding genes, non-coding genes, or neutral seq...e for aligning two bird-size genomes (~1.2 Gb) is around two da...mp; Lindblad-Toh, K. (2010). Genome-wide synteny through highly...2971 days ago
PolyPhen-2: Prediction of functional effects of human nsSNPs
PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.2961 days ago
Hagfish - assess an assembly through creative use of coverage plots
...equencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification...2964 days ago
RCircos: an R package for Circos 2D track plots
...lots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also...2964 days ago
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
...n sequencing reads to a reference genome. Uniquely among current map...ted by all the major sequencing technologies, including Illumina, Ap...the generated data (sequencing technologies, low-coverage and exome...ides explicit support for handling known-sequence SVs, e.g. mobile e...2964 days ago
