Search Results for "mummer"

Eight PERL scripts. remap_qualifiedASM.pl strict_filter.pl - Refine the MUMmer alignment aln_extract.pl - Extract sequence from MUMmer alignment core_genome_build.pl - Build (relaxed) core genome based on sequences in MUMmer alignment core_remove_region.pl - Remove repetitive regions or other regions core_map2snp.pl - Extract SNPs from the core genome nucmer_filter.pl - A integrated script that run MUMmer to generate a mapped sequence core_snp2fas.pl - Build a SNP-only alignment based on SNPs extracted.

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc.

MUMmerGPU is a high-throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. It aligns sequences in parallel on the video card to accelerate the widely used serial CPU program MUMmer.

Parallel version of MUMMER v. 3.14, a genome-level alignment tool used to assemble complete genomes.