Results for "mummer"
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...ata other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or i...2866 days ago
- .... In addition to SAM and BAM files with long, short, or paired-end reads, Ribbon can also load coordinate files from whole genome aligners such as MUMmer. Therefore, Ribbon can be use...
2800 days ago
CISA: Contig Integrator for Sequence Assembly
...s generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on...2745 days ago
GARM:Genome Assembly, Reconciliation and Merging
...he pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages...2741 days ago
MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
...following tools installed and in $PATH, or added to $binpath in the tool: Newbler (specifically runAssembly)Minimus2 (part of AMOS, also requires MUMmer)2741 days ago
- ...aps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions a...rate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating progra...
2682 days ago
Dot, an interactive viewer for genome-genome comparison
...alize genome-genome alignments in order to evaluate new assemblies and perform exploratory comparative genomics. Dot supports the output of MUMmer’s nucmer aligner the mo...2350 days ago
MUMmer4: A fast and versatile genome alignment system
MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by c...t suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and...oretical limit on the input size of 141Tbp, MUMmer4 can now work with input sequ...2330 days ago
- Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch...FERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter probl...
2199 days ago
mScaffolder: A comparative genome scaffolding tool
A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high...e as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients t...2198 days ago
