David Coil

@davidacoil

Project scientist in the Eisen () lab (microbial ecology/genomics) ; outreach and undergraduate education. Also Ground Truth Trekking non-profit.

Davis, CA
microbe.net
Joined June 2010
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  1. 16 minutes ago

    Is there any good way to scrape sample origin information from a bunch of WGS projects at NCBI? If for example I wanted to ask the question "where do the sequenced strains of species X come from?".

    1 like
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  2. 12 hours ago

    The switch from bacterial isolate genomes I've looked at (100's) to MAGs (just starting) is hard. I think they all look incomplete and crappy. And those without 16S pain me...

    1 reply 3 likes
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  3. Retweeted
    Apr 2

    I'm hiring a bioinformatics programmer! This will be a fun agtech position in Davis, CA. Have a big impact in a small company, lots of room to grow. Focus will be on comparative microbial genomics and/or microbiome analysis. All levels considered.

    6 replies 65 retweets 36 likes
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  4. Apr 2

    This was on my desk today, from . May be just what we needed to get long reads!

    1 retweet 14 likes
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  5. Mar 31

    One of our star undergrads, Karley Lujan, tried her hand at blogging some background related to her work.

    1 retweet 2 likes
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  6. Mar 29

    I finally got around to reading the GTDB paper "A proposal for standardized bacterial taxonomy based on genome phylogeny". What do people think? Is this the new taxonomy or a flash-in-the-pan?

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  7. Mar 29

    Finally read "KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples". Think it should be mandatory reading, not for wet lab portion necessarily but for use of controls.

    1 reply 14 retweets 22 likes
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  8. Retweeted
    Mar 28

    Anyone have recommendations for a mock community standard to use as a positive control for 16S sequencing? Commercial products or homebrew?

    6 replies 6 retweets 10 likes
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  9. Retweeted
    Mar 28

    Woohoo - we got our new MinIon for the lab - can someone help me figure out how to use it for sequencing ?

    5 replies 10 retweets 122 likes
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  10. Retweeted
    Mar 28

    Wait a sec - hey said the minion was small - I can’t use this thing for portable sequencing

    3 replies 3 retweets 46 likes
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  11. Mar 28

    My post about the bath toy microbiome study.

    1 reply 1 retweet 5 likes
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  12. Retweeted
    Mar 28

    Hey - you could play a huge role in the portrayal of women in science. How about rewriting this story and actually name the woman who did the study, instead of 2 male scientists who were not even involved? Her name is Lisa Neu.

    23 replies 591 retweets 1,411 likes
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  13. Mar 27

    Currently reading the very excitingly titled "A comprehensive toolkit to enable MinION sequencing in any laboratory". Sounds like just what we need!

    1 reply 5 retweets 14 likes
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  14. Mar 24

    New tool of interest: GraftM: “a tool for scalable, phylogenetically informed classification of genes within metagenomes”

    7 retweets 12 likes
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  15. Mar 23

    "An informative glimpse into the drug factory microbiome: Which bugs coexist with our drugs? The story behind the paper"

    2 retweets 2 likes
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  16. Mar 22

    New paper of interest on Hospital Plumbing and Carbapenem Resistance

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  17. Retweeted
    Mar 22
    Replying to and

    As promised, near perfect bacterial genome sequence with See the preprint here:

    1 reply 11 retweets 16 likes
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  18. Retweeted
    Mar 21
    Replying to

    Great blog post. The original tweet was definitely ... fun. If you decide to test PacBio let me know. We have some pretty polished solutions and upcoming improvements should make the cost v Illumina pretty attractive. Tools/protocols exist for high quality PacBio-only assemblies.

    1 reply 1 retweet 1 like
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  19. Mar 21

    My musings on and attempted summary of the Twitter discussion last week regarding Pacbio vs Illumina, vs Nanopore for bacterial genome assembly. Comments welcome!

    5 replies 19 retweets 34 likes
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  20. Retweeted
    Mar 20

    I decided that ‘Unsolicited Gratitude’ is one of my 2018 goals, and my way of giving back to people after the last few rough/stressful years. First recipients (unsuspecting victims?) are - FedEx box coming your way this week!!

    4 replies 2 retweets 31 likes
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