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  1. Registration reminder for our two-week summer workshop on high-throughput sequencing data analysis!

    Our two-week summer workshop (announcement, direct link) is shaping up quite well, but the application deadline is today! So if you're interested, you should apply sometime before the end of the day. (We'll leave applications open as long as it's March 17th somewhere in the world.)

    Some updates and expansions …

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  2. Some ideas for workshops and unconference models for data-intensive biology

    Here at the Lab for Data-Intensive Biology (TM) we are constantly trying to explore new ideas for advancing the practice of biological data sciences. Below are some ideas that originated with or were sharpened by conversations with Greg Wilson (Executive Director, Software Carpentry) and Tracy Teal (Project Lead, Data Carpentry …

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  3. Assembling the heck out of soil - paper posted

    We just posted yet another pre-submission paper to arXiv.org:

    Assembling large, complex environmental metagenomes

    Authors: Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah Tringe, James M. Tiedje, and C. Titus Brown

    arXiv link

    Paper repository on github

    Abstract:

    The large volumes of sequencing data required to deeply sample …
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  4. Assembly artifacts paper posted

    We just posted another pre-submission paper to arXiv.org:

    Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets

    Authors: Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning, Rachel Mackelprang, Susannah Tringe, Janet Jansson, James M. Tiedje, and C. Titus Brown

    arXiv link

    Paper repository on github

    Abstract:

    Sequencing errors and …
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  5. Some early experience in teaching using ipython notebook

    As part of the 2012 Analyzing Next-Generation Sequencing Data course, I've been trying out ipython notebook for the tutorials.

    In previous years, our tutorials all looked like this: Short read assembly with Velvet -- basically, reStructuredText files integrated with Sphinx. This had a lot of advantages, including Googleability and simplicity; but …

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  6. Paper draft: Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

    (updated to point to http://arxiv.org/).

    Authors: Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown

    Abstract:

    The memory requirements for de novo assembly of short-read shotgun sequencing data from complex microbial populations are an increasingly large practical barrier to environmental studies. Here we …
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