Results for "genome assembly"
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...Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”.&nbs...2926 days ago
SATSUMA : Highly sensitive whole-genome synteny alignments.
Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only t...res. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days...Di Palma, F., & Lindblad-Toh, K. (2010). Genome-w...2926 days ago
Hagfish - assess an assembly through creative use of coverage plots
...ilds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment. Hagf...2918 days ago
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mappi...technologies, low-coverage and exome) in the 1000 Genomes...2918 days ago
- Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome....
2918 days ago
Stand-alone programs for Bioinformatician
This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine. For help on the bigBed and bigWig applications see:http://genome.ucsc.edu/goldenPath/help/bigBed.htmlhttp://genome.u...2917 days ago
- methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. Th...tion data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome b...
2904 days ago
- ...s (TAGC plots) to visualise the contents of genome assembly data sets as a QC step Bla...s (TAGC plots) to visualise the contents of genome assembly data sets as a QC step. This...sented in the paper to create a preliminary assembly, and to create and collate GC...
2894 days ago
- ...porting (GAEMR) package is an assembly analysis framework composed...ness -- how many pieces in an assembly composed of, how wel...eces accurately represent the genome sequenced, and how much of that genome is represented by those pieces....of the condition of a genome assembly. ...
2894 days ago
CovCal: Coverage / Read Count Calculator
Coverage / Read Count Calculator Calculate how much sequencing you need to hit a targe...nstructions: set the read length/configuration and genome size, then select what you wa...C = Coverage (X),L = Read length (bp), G = Haploid genome s...2178 days ago
