1. My new data analysis pipeline code

    First, I write a recipe file, 'metagenome.recipe', laying out my job description for, say, sequence trimming and assembly with Velvet:

    fasta_file soil-data.fa
    
    qc_filter min_length=50 remove_Ns=true
    
    graph_filter min_length=400
    
    velvet_assemble k=33 min_length=1000 scaffolding=True
    

    Then I specify machine parameters, e.g. 'bigmem.conf':

    [defaults]
    n_threads …
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  2. The last five years

    Looking back, the last 5 years have, collectively, been rather overwhelming.

    Five years ago, I was a big-mouthed 7th year graduate student. The biggest change in my recent life was getting a cat (first) and getting married (second).

    Now, I'm the father of two (adorable) daughters. I have a minivan …

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  3. What's in it for me? Thoughts on open science.

    If you've been under a rock (or indulging in arsenic yourself), you've heard about NASA's "arsenic" article, claiming the discovery of a microbial species that can substitute arsenate for phosphate. The paper was pre-announced via a press conference that then announced the results.

    Immediate blogtastrophe! The paper was critically reviewed …

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