Genovo: De Novo Assembly for Metagenomes (Record no. 47466)

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control field MX-MdCICY
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control field 20250625153919.0
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Transcribing agency CICY
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Classification number (OCLC) (R) ; Classification number, CALL (RLIN) (NR) B-13265
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Title Genovo: De Novo Assembly for Metagenomes
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Volume/sequential designation Journal of Computational Biology, 18(3), p.429-443, 2011
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Summary, etc. Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A nonparametric prior accounts for the unknown number of genomes in the sample. Inference is performed by applying a series of hillclimbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs in a series of synthetic experiments and across nine metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, even for low-abundance sequences, and yield a higher assembly score. Supplementary Material is available at www.liebertoinline.com/cmb.
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Topical term or geographic name entry element ALGORITHMS
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Topical term or geographic name entry element CANCER GENOMICS
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Topical term or geographic name entry element SEQUENCES
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Personal name Laserson, J.
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Personal name Jojic, V.
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Personal name Koller, D.
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Uniform Resource Identifier <a href="https://drive.google.com/file/d/1R3Bc_HMkTHJNhLTxJCY2wySvtbuDH-eF/view?usp=drivesdk">https://drive.google.com/file/d/1R3Bc_HMkTHJNhLTxJCY2wySvtbuDH-eF/view?usp=drivesdk</a>
Public note Para ver el documento ingresa a Google con tu cuenta: @cicy.edu.mx
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Source of classification or shelving scheme Clasificación local
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  Clasificación local     Ref1 CICY CICY Documento préstamo interbibliotecario 25.06.2025   B-13265 25.06.2025 25.06.2025 Documentos solicitados