Metagenomic assembly and annotation
Microbial profiling using metagenomic assembly
... when applied to novel or poorly described taxa. As future efforts continue to expand the content of public databases these biases will diminish. A related but much more minor limitation with the use of resources such as ...
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MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
... that assembly is just one of many other bioinformatics analyses typically performed in metagenomic projects, including taxonomic classifica- tion, gene annotation, variant analysis, and so ...
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Xander: employing a novel method for efficient gene-targeted metagenomic assembly
... targeting assembly of specific protein-coding ...standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation ...weighted ...
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MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
... precise annotation for reads and more incorrect annotation for contigs - Even though the reads/contigs are from a particular species, they may be aligned to similar but different species under the same ...
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MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
... precise annotation for reads and more incorrect annotation for contigs - Even though the reads/contigs are from a particular species, they may be aligned to similar but different species under the same ...
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Virome assembly and annotation: A surprise in the Namib Desert
... However, comparative analyses assessing the efficiency of these procedures are still outstanding. Despite severe environmental constraints, deserts host a multitude of animals, plants, and microorganisms, and are ...
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A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling
... of metagenomic (MG) and metatranscriptomic (MT) ...processing, assembly, taxonomic characterisation, gene finding, protein-coding gene annotation and pathway reconstruction, such as MinPath [16], ...
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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
... a full taxonomy list. Our MAG annotation pipeline is available as a reproducible workflow 76 . Genomes and gene predictions were loaded into a Meta4 database 77 The cleaned bins were compared, using MinHash ...
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Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria
... manual annotation of the metagenome bin revealed that “Spartobacteria baltica” uses a set of pathways typical of many aerobic heterotrophic organisms (see Table S3 in the supplemental ...
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Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation
... such annotation efforts may be enhanced by assembling reads into longer contiguous sequences ( ‘ contigs ’ ), prior to database search ...current assembly pipelines perform for metatranscriptomic ...the ...
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Metagenomic analysis of silage
... . Metagenomic sequence data is analyzed by an ever-increasing range of bioinformatic ...novo assembly of sequence reads to contigs and scaffolds 30,31 , taxonomic classification and visualization of ...
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Metagenomic Assembly
... Advancing Science with DNA Sequence The World’s Greatest Science Protecting America.. Metagenomic Assembly.[r] ...
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Unbiased taxonomic annotation of metagenomic samples
... taxonomic annotation of metagenomic samples, which is usually done by first mapping the reads to the reference sequences and then, classifying each read at a node in the clade of the LCA of the candidate ...
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Unbiased taxonomic annotation of metagenomic samples
... a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate ...
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A safe and complete algorithm for metagenomic assembly
... assembled those paths whose internal nodes have out- degree equal to one, with no restriction on their in- degree. Other strategies such as [9, 21, 22] are based on iteratively reducing the assembly graph, for ...
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The Viral MetaGenome Annotation Pipeline (VMGAP): An automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
... so included in the non-redundant protein database, entries in the former have a higher priority since they are curated and therefore provide better func- tional annotation. Hits against HMMs describing AC- LAME ...
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MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets
... to assembly of sequenced DNA fragments ...efficient assembly of metagenomic sequence ...of metagenomic sequence ...of assembly for generating the final set of ...real-world ...
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Assembly and repeat annotation of the nothobranchius furzeri genome
... I created three independent N. furzeri repeat libraries using different datasets and compared their potential to detect repeats in the genome assembly. To create the library RModLib, RepeatModeler performed a de ...
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Assessment of metagenomic assembly using simulated next generation sequencing data
... of metagenomic assemblies of next generation sequencing methods (pyrosequencing and Illu- mina) and compare these to classical Sanger sequencing as well as to previous ...new metagenomic simulators iMESS ...
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Ten steps to get started in Genome Assembly and Annotation
... genome annotation pipeline is almost always in GFF ...the annotation process, the sequence of these fea- tures can however easily be ...and annotation and are often used when submitting ...
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