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...es. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days...i Palma, F., & Lindblad-Toh, K. (2010). Genome-wide s...2966 days ago
Hagfish - assess an assembly through creative use of coverage plots
Hagfish is a tool that is to be used in dat...quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment. Hagfish requires...e sequence and a paired end re-sequencing data set. Hagfish has more po...2959 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 Proje...2959 days ago
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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.ucsc.e...2957 days ago
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CovCal: Coverage / Read Count Calculator
Coverage / Read Count Calculator Calculate how much sequencing you need to hit a targ...structions: set the read length/configuration and genome size, then select what you wa... = Coverage (X),L = Read length (bp), G = Haploid genome size (...2218 days ago