Results for "Genome"

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  • PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.

    We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, thos...

    Tags: PRICE, Paired-Read, Iterative, Contig, Extension, de novo, genome, assembler, C++.

    2117 days ago

  • assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference genome

    Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X f...

    Tags: assemblytics, delta, analyze, alignment, assembly, reference, genome, visualization

    2114 days ago

  • Download blasr 1.3 version

    DOWNLOAD LINK: https://github.com/BioInf-Wuerzburg/proovread/raw/master/util/blasr-1.3.1/blasr I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error: fail to open file './temporarySam' [bwa_aln_core] write to the disk... 0.09 sec[bwa_aln_core] 70778880 sequences ha...

    Tags: blasr, download, scaffolder, OPERA-LG, temporarySam, genome, contigs

    2113 days ago

  • getopts.pl file

    SSPACE_longread complain for getopts.pl file. To resolve this, download and have in SSPACED-Longreads folder. Cheers :)

    Tags: SSAPCE, LongREads, SSPACE-Longreads, Scaffolding, error, getopts, perl, genome

    2113 days ago

  • mScaffolder: A comparative genome scaffolding tool

    A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to th...

    Tags: mScaffolder, comparative, genome, scaffolding, tool, genome, contigs, scaffolds

    2113 days ago

  • LINKS scaffolder bloomfilter setting !

    ➜ bin git:(master) ✗ ls -l total 68 drwxrwxr-x 3 urbe urbe 4096 Jun 15 12:15 lib -rwxrwxrwx 1 urbe urbe 65141 Jun 15 17:13 LINKS ➜ bin git:(master) ✗ pwd /home/urbe/Tools/LINKS_1.8.6/bin ➜ bloomfilter git:(master) ✗ swig -Wall -c++ -perl5 BloomFilter.i ➜ bloomfilter git:(master) ✗...

    Tags: LINKS, scaffolder, genome, Perl, Perl_Gthr_key_ptr, setting, anaconda

    2113 days ago

  • JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

    JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes a...

    Tags: JBrowse, Embeddable, genome, browser, genome, reads, view, map, JavaScript, HTML5

    2099 days ago

  • ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data

    ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k...

    Tags: ChopStitch, exon, annotation, splice, graph, transcriptome, assembly, whole, genome, sequencing

    2095 days ago

  • KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

    KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting. gcp: K-mer GC Pr...

    Tags: KAT, K-mer, analysis, toolkit, quality, control, NGS, datasets, genome, assemblies

    1944 days ago

  • Genome U-Plot: a whole genome visualization

    Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution an...

    Tags: Genome, U-Plot, whole, genome, visualization

    2084 days ago