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7 results for “genome assembly, genome assembly evaluation”
Genome assemblies for "Versatile genome assembly evaluation with QUAST-LG"
<p>Supplementary data for A. Mikheenko, A. Prjibelski, V. Saveliev, D. Antipov, A. Gurevich. Versatile genome assembly evaluation with QUAST-LG. ISMB 2018 PROCEEDINGS (<em>Bioinformatics </em>journal)</p> <p>Reference genomes of</p> <ol> <li><em>Saccharomyces cerevisiae </em>(yeast) version R64-1-1 </li> <li><em>Caenorhabditis elegans </em>(worm) version WBcel235</li> <li><em>Drosophila melanogaster </em>(fruit fly) version BDGP6</li> </ol> <p>And<em> de novo</em> genome assemblies of</p> <ol> <li>Yeast_PB (<em>S. cerevisiae</em>, genome size: 12.1 Mb): Canu, FALCON, Flye, MaSuRCA, Miniasm (from Illumina pair-ends and PacBio SMRT)</li> <li>Yeast_NP (<em>S. cerevisiae</em>, genome size: 12.1 Mb): Canu, Flye, MaSuRCA, Miniasm (from Illumina pair-ends and Oxford Nanopore)</li> <li>Worm_PB (<em>C. elegans</em>, genome size: 100.3 Mb): Canu, FALCON, Flye, MaSuRCA, Miniasm (from Illumina pair-ends and PacBio SMRT)</li> <li>Fly_MP (<em>D. melanogaster</em>, genome size: 137.6 Mb): ABySS2, MaSuRCA, Meraculous, Platanus, SOAPdenovo2, SPAdes (from Illumina pair-ends and mate-pairs)</li> <li>Human_MP (<em>H. sapiens</em>, genome size: 3.1 Gb): UpperBound assembly only (from Illumina pair-ends and mate-pairs)</li> <li>Human_NP (<em>H. sapiens</em>, genome size: 3.1 Gb): UpperBound assembly only (from Illumina pair-ends and Oxford Nanopore)</li> </ol> <p>Each pack (items 1-4) is accompanied with the upper bound assembly created with QUAST-LG (for computing theoretical limits on assembly correctness and completeness for a particular genome and set of reads). For more information, interactive QUAST-LG reports, and links to <em>de novo</em> assemblies of the human datasets please visit http://cab.spbu.ru/software/quast-lg/ or write to <em>quast.support@cab.spbu.ru.</em></p>
An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce (Picea abies)
<p>Data files for construction of the haploid genetic map for Norway spruce (<em>Picea abies</em>). Available at <a href="https://doi.org/10.1101/292151">https://doi.org/10.1101/292151</a></p>
Supplementary data for "WebQUAST: online evaluation of genome assemblies"
<p>Supplementary data for A. Mikheenko, V. Saveliev, P. Hirsch, A. Gurevich. WebQUAST: online evaluation of genome assemblies.</p> <p><br> Reference genomes of two <em>Escherichia coli</em> K-12 substrains (MG1655 and W3110) and genome annotation of MG1655.</p> <p><em>De novo</em> assemblies of the <em>Escherichia coli</em> K-12 MG1655 short-read Illumina dataset (<a href="https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=ERR008613&display=metadata">ERR008613</a>) with ABySS, MEGAHIT, SPAdes, and Velvet.</p> <p>WebQUAST reports in three evaluation modes: <br> * Use Case 1: reference-free evaluation (<em>sample_data_no_ref</em>)<br> * Use Case 2: reference-based evaluation (<em>sample_data_true_ref</em>) <br> * Use Case 3: evaluation based on a close reference (<em>sample_data_close_ref</em>)</p> <p>The snapshot (<a href="https://github.com/ablab/quast/commit/2bd50600bcf63ee826965c10f6ca4cdc2aa046e5">commit 2bd5060</a>) of the QUAST command-line version used by WebQUAST for generating the reports.</p>
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies
<p>The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.</p>
A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies
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Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki
<p>For any genome-based research, a robust genome assembly is required. <em>De novo</em> assembly strategies have evolved with changes in DNA sequencing technologies and have been through at least three phases: i) short-read only, ii) short- and long-read hybrid, and iii) long-read only assemblies. Each of the phases has their own error model. We hypothesized that hidden scaffolding errors in short-read assembly and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of <em>T. borchgrevinki</em> from data generated during each of the three phases and assessed the quality problems we encountered. We developed strategies such as k-mer-assembled region replacement, parameter optimization, and long-read sampling to address the error models. We demonstrated that a k-mer-based strategy improved short-read assemblies as measured by BUSCO while mate-pair libraries introduced hidden scaffolding errors and perturbed BUSCO scores. Further, we found that although hybrid assemblies can generate higher contiguity, they tend to suffer from lower quality. In addition, we found long-read-only assemblies can be optimized for contiguity by sub-sampling length-restricted raw reads. Our results indicate that long-read contig assembly is the current best choice and that assemblies from phase I and phase II were of lower quality.</p>
Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki
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