Optimizing de novo genome assembly from PCR-amplified metagenomes

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@JulesRKM @JMA_Stough @szetoinsitu Yes, plus PCR-amplified libraries will lead to uneven coverage, which may make it difficult to identify misassemblies (https://t.co/33wzO2ZxOE). And amplification can also create chimeric DNA and/or RNA templates (which will look perfectly fine from an assembly point of view).
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@SieraVirus @SaritAvrani Ella, I have done extensive testing with it for viromes & plan to publish a second paper this year on how it compares. In short it is not terrible but can be affected by PCR cycle #. DM me if you want to chat more. Here is the first paper with a some info https://t.co/l47bRzY4Iz
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1852 days ago
RT @simroux_virus: @merenbey @ReiterTaylor @campanarostef @BioMickWatson The "good" news: biases from "too-many-PCR" seem to be insert size…
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@merenbey @ReiterTaylor @campanarostef @BioMickWatson The "good" news: biases from "too-many-PCR" seem to be insert size related, so kind of homogeneous between genomes (https://t.co/33wzO2ZxOE) i.e. you can still use the metaG to have a rough approximation of relative abundance of genome A vs B (as seen in https://t.co/72NUCxWsLb)
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2072 days ago
RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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2072 days ago
Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metagenomes" @thePeerJ by @gtrubl @simroux_virus @Lab_Sullivan @northenlab and others: https://t.co/7BGIhLlptq. @LBNLBioSci @BerkeleyLab @Livermore_Lab
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2074 days ago
RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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2077 days ago
RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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2078 days ago
Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metagenomes" @thePeerJ by @gtrubl @simroux_virus @Lab_Sullivan @northenlab and others: https://t.co/7BGIhLlptq. @LBNLBioSci @BerkeleyLab @Livermore_Lab
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RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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RT @jgi: Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metageno…
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2080 days ago
Linked in our latest @jgi Genome Insider #podcast episode, revisit "Optimizing de novo genome assembly from PCR-amplified metagenomes" @thePeerJ by @gtrubl @simroux_virus @Lab_Sullivan @northenlab and others: https://t.co/7BGIhLlptq. @LBNLBioSci @BerkeleyLab @Livermore_Lab
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2093 days ago
RT @gtrubl: Catching up on work from vacation. Optimizing bioinformatics yields more robust virus genomes. SPAdes has been getting a lot of…
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Optimizing de novo genome assembly from PCR-amplified metagenomes https://t.co/W435lacCPR | https://t.co/MDvk5e07PE | https://t.co/pnxDltJLsh
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RT @gtrubl: Catching up on work from vacation. Optimizing bioinformatics yields more robust virus genomes. SPAdes has been getting a lot of…
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RT @gtrubl: Catching up on work from vacation. Optimizing bioinformatics yields more robust virus genomes. SPAdes has been getting a lot of…
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RT @gtrubl: Catching up on work from vacation. Optimizing bioinformatics yields more robust virus genomes. SPAdes has been getting a lot of…
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RT @gtrubl: Catching up on work from vacation. Optimizing bioinformatics yields more robust virus genomes. SPAdes has been getting a lot of…
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Catching up on work from vacation. Optimizing bioinformatics yields more robust virus genomes. SPAdes has been getting a lot of attention for being the 'best' assembler for virus contigs & here we show sc>meta option (1 part of the paper). https://t.co/l47bRzY4Iz @simroux_virus
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2421 days ago
RT @Ahlgren_lab: I'm slow on the tweet here, but glad to be a [very] small part of this work by @simroux_virus and others: Assembly of PCR-…
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RT @Ahlgren_lab: I'm slow on the tweet here, but glad to be a [very] small part of this work by @simroux_virus and others: Assembly of PCR-…
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I'm slow on the tweet here, but glad to be a [very] small part of this work by @simroux_virus and others: Assembly of PCR-amplified metagenomes https://t.co/i8ILE8AIQ1 via @thePeerJ @simroux_virus @Lab_Sullivan @JedFuhrman
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