• The mothur AMI

    Do you find that your computer can no longer handle the massive datasets that you are running? Does your institution not have a computer cluster? Welcome to the wonderful world of the Amazon Web Server.

  • Customize your reference alignment for your favorite region

    You threw caution to the wind and decided to sequence something other than the V4 region of the 16S rRNA gene. How do you pick the start and end coordinates when running pcr.seqs?

  • mothur and QIIME

    mothur and QIIME have had an exceptional impact on the field of microbial ecology and helped lead the ongoing explosion of interest in studying the human microbiome. I've refrained from publicly making any comparisons between the two programs because I knew that anything I said would be appropriately viewed with suspicion. So, what do I think of QIIME?

  • Suck until you don't

    I am often asked how to get better at something. It is a great honor for someone else to recognize a set of skills that I work hard to hone, but I honestly want to answer "the hell if I know." Last week I talked with someone that was interested in strengthening their programming skills and perhaps converting some of their home grown code into a package for others to use. For the first time I answered honestly, "You're going to suck, but it will get better."

  • README for the SILVA v123 reference files

    The good people at SILVA have released a new version of the SILVA database. A little bit of tweaking is needed to get their files to be compatible with mothur. This README document describes the process that I used to generate the mothur-compatible reference files.

  • What is your microbiome hypothesis worth?

    Last week I attended a symposium geared towards a general science audience where the topic of the day was the role of the microbiome in human health. I would exaggerate only slightly if I said that all of the presenters motivated their own interest in the microbiome by citing the work of Turnbaugh and colleagues from the Gordon lab pointing to differences in diversity and the ratio of Firmicutes and Bacteroidetes among lean and obese individuals. Similar sets of introductory slides probably grace most talks at these types of symposia. Lost in the hubbub about the microbiome and obesity are two very important papers (here and here) - one of which was written by an author on the original study - saying that the effect doesn't exist when you consider any other dataset. Yet as of my writing, there is nothing on PubPeer or PubMed Commons directing readers of the original paper to these meta-analyses.

  • Why did I publish in mSphere?

    On the morning of September 14th, I logged into mSphere's manuscript submission page and uploaded a very cool paper describing our efforts to model the number of colonic tumors in a mouse model of colorectal cancer based on the composition of the animals' microbiota 70 days earlier. I'm very proud of the paper that I wrote with my former graduate student Joe Zackular. But I'm also very proud of the manuscript tracking number we received: mSphere00001-15. Our's was the first paper to be submitted and then eventually accepted at the new journal being published by the American Society for Microbiology.

  • Initial reactions to the UMU & IMI

    I must admit that I always feel a certain euphoria when I find people talking about microbiome research in the popular press or policy pieces. I'm a microbiome homer. So you can imagine my feelings yesterday when Science published an article by US scientists calling for a "interdisciplinary Unified Microbiome Initiative (UMI) to discover and advance tools to understand and harness the capabilities of Earth’s microbial ecosystems." Not to be outdone, Nature published a piece indicating that each country would have its own UMI and these would be assembled under an International Microbiome Initiative (IMI).

  • No, greengenes' reference alignment hasn't improved

    An under appreciated, but important component to assigning sequences to OTUs is generating a sequence alignment. As with many things in the world of microbiome analysis, there is a spectrum of options. In case you've missed it, I've published three papers in the last few years on this topic. These papers all point to the importance of aligning your data and are the justification for how we run align.seqs in the MiSeq SOP and the 454 SOP. Over the weekend some questions came up about aligning 16S rRNA gene sequences that I thought worth expanding up on here.

  • My response to the OSTP's RFI on the microbiome

    The Office of Science and Technology Policy (OSTP) recently released a request for information (RFI) to "to solicit feedback from industry, academia, research laboratories, and other stakeholder groups on both the overarching questions that unite all microbiome research and the tools, technologies, and training that are needed to answer these questions." This is a draft of a letter that I will be submitting regarding the need for bioinformatic tool development, continued software maintenance, and training.

  • README for the RDP v14 reference files

    The good people at the RDP have released a new version of the RDP database. A little bit of tweaking is needed to get their files to be compatible with mothur. This README document describes the process that I used to generate the mothur-compatible reference files. The original files are available from the RDPs sourceforge server and were used as the starting point for this README.

  • Happy mothur's day!

    At least in the United State's, Sunday was Mother's Day. The day we acknowledge the women that brought us into the world and the women that have helped care for us. Happy belated Mother's Day! We also love to mark Mother's Day as mothur's Day. When I can remember, I try to do something special to mark the date.

  • We need a mothur logo (and stickers!)

    Have you noticed that the same poor woman has been nursing an unknown child on the mothur wiki since the beginning of the project? That's my wife and Schloss kid #4. Although she is now world renowned and forever linked with mothur, that picture doesn't make for a very good logo. Would you like to help us do something about this?

  • We don't read about dinosaurs

    To be perfectly frank, I think bioinformatics and the problems most of us are interested in are pretty abstract. Worse, they're pretty boring. Try going to a party and talk about the latest greatest way of assembling a genome. Try going to your kids school and tell them about why you think we should or shouldn't use a 3% cutoff to define a bacterial OTU. You might bring some caffeine pills with you. So what makes bioinformatics, computer science, and math interesting? Cool examples.

  • The Kitome: Dealing with the reagent microbiome

    An important paper came out this week that everyone should be well aware. It went through the somewhat boring task of sequencing negative controls. Right now you're yawning, right? You might want to read the paper and go check that paper you just published to see if any of the bugs you claimed were responsible for your disease du jour were mentioned. We'll wait...

  • README for the RDP v10 reference files

    The good people at the RDP have released a new version of the RDP database. A little bit of tweaking is needed to get their files to be compatible with mothur. This README document describes the process that I used to generate the mothur-compatible reference files. The original files are available from the RDPs sourceforge server and were used as the starting point for this README.

  • MicroSeminar: A new way of doing conferences

    Why didn't I think of that?! In the last few years I've pretty much lost all my drive to go to conferences to give talks. So when I saw a Twitter post from Jennifer Biddle (UDel) this summer announcing the creation of the MicroSeminar, I got excited. After seeing the seminar series roll out over the summer I noticed they have had a very "environmental" focus to the initial talks. I offered my services to give a microbiome-based microbial ecology talk and viola! My talk will be this Friday (10/17/2014) at 11 AM eastern. You can watch it through their Google+ site and later through their YouTube channel.

  • Why do I have such a large distance matrix?

    One of the more common questions we get on the mothur forum and to the mothur.bugs email list is some variant of, "My distance matrix takes up 100 GB and it won't go through cluster or cluster.split to make OTUs. What can I do?" Having answered some variant of this question 1000 times, I fear that I might stroke out if I answer it a 1001st time. So, allow me to explain what's going on, what you should have done, what you can do, what you should do, and why you should care. I'll try not to rant... to much.

  • Slides for Illumina Users Meeting talk

    Pat will be giving a talk today about the MiSeq protocol he developed for sequencing the 16S rRNA gene at the Illumina Users Meeting in Columbus, OH. His slides are available through his github website

  • Slides for EDAMAME mothur talk

    Pat will be giving a talk about mothur at Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) Workshop this friday. You can learn more about the workshop through the EDAMAME website.

  • README for the greengenes v13_8_99 reference files

    The greengenes developers periodically update their reference files on their ftp server. What follows is our process for generating a mothur-compatible set of files to generate a greengenes taxonomy reference of those sequences.

  • README for the SILVA v119 reference files

    The good people at SILVA have released a new version of the SILVA database. A little bit of tweaking is needed to get their files to be compatible with mothur. This README document describes the process that I used to generate the mothur-compatible reference files.

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