Results for "Genome"

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  • MUMmer4: A fast and versatile genome alignment system

    MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. With a theoretical limi...

    Tags: MUMmer4, fast, versatile, genome, alignment, system

    2246 days ago

  • GenomeTools: The versatile open source genome analysis software

    The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules. If ...

    Tags: GenomeTools, versatile, open, source, genome, analysis, software

    2242 days ago

  • Carefully opt for human reference genome

    Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the following: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/00...

    Tags: Carefully, opt, human, reference, genome

    1501 days ago

  • ARCS: scaffolding genome drafts with linked reads

    ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromi...

    Tags: ARCS, scaffolding, genome, drafts, linked, reads

    2214 days ago

  • G-compass: a comparative genome browser

    G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their o...

    Tags: G-compass, comparative, genome, browser, visualization

    2178 days ago

  • AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

    AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --...

    Tags: AlignGraph, algorithm, secondary, de novo, genome, assembly, guided, references

    2172 days ago

  • Metassembler: merging and optimizing de novo genome assemblies

    Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have ...

    Tags: Metassembler, merging, optimizing, de novo, genome, assemblies, tools

    2152 days ago

  • MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

    MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for e...

    Tags: MECAT, fast mapping, error correction, de novo, assembly, genome, single-molecule, sequencing, reads, Tools

    2149 days ago

  • Circlator: automated circularization of genome assemblies using long sequencing reads

    A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-08...

    Tags: Circlator, automated, circularization, genome, assemblies, sequencing, reads

    2145 days ago

  • CrossMap: a program for convenient conversion of genome coordinates

    CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWi...

    Tags: CrossMap, program, convenient, conversion, genome, coordinates

    2129 days ago