Results for "Assembly"

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  • HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly

    HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliabl...

    Tags: HaploMerger2, rebuild, haploid, sub-assemblies, high-heterozygosity, diploid, genome, assembly

    2009 days ago

  • Long read assembly workshop !

    This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data....

    Tags: longread, ngs, assembly, genome, reads, tutorial

    2002 days ago

  • QUAST-LG: Versatile genome assembly evaluation

    QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for ...

    Tags: QUAST-LG, Versatile, genome, assembly, evaluation

    1981 days ago

  • LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

    LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the pa...

    Tags: LR_Gapcloser, tiling, path-based, gap, closer, long, reads, complete, genome, assembly

    1414 days ago

  • Referee: Genome assembly quality scores

    Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality sc...

    Tags: Referee, Genome, assembly, quality, scores, ngs

    1971 days ago

  • SKESA: strategic k-mer extension for scrupulous assemblies

    SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast,...

    Tags: SKESA, strategic, k-mer, extension, scrupulous, assemblies, genome, assembly

    1961 days ago

  • MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

    MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accele...

    Tags: MEGAHIT, ultra-fast, single-node, solution, large, complex, metagenomics, assembly, succinct, de Bruijn, graph

    1961 days ago

  • Genobuntu: A software package containing more than 70 software and packages oriented towards NGS and genome assembly

    Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assemb...

    Tags: Genobuntu, software, package, packages, oriented, NGS, assembly, genome

    1934 days ago

  • ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data

    The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC,...

    Tags: ALLHiC, Phasing, scaffolding, polyploid, genomes, Hi-C, data, assembly

    1925 days ago

  • Versatile genome assembly evaluation with QUAST-LG

    QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST  package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large ...

    Tags: Versatile, genome, assembly, evaluation, QUAST-LG

    1924 days ago