The second iteration of our bioinformatics summer course, Analyzing Next-Generation Sequencing Data, just finished. It was a great success, at least judging from the comments that people made to us personally; the evaluations aren't yet complete.
The what: a two week course on analyzing next-gen sequencing data, using the Amazon …
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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 …read more
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I just parachuted in on (and heli'd out of?) the Beyond the Genome conference in Boston. I gave a very brief workshop on using EC2 for sequence analysis, which seemed well received. (Mind you, virtually everything possible went wrong, from lack of good network access to lack of attendee computers …
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(with Adina Howe, Jason Pell, Rosangela Canino-Koning, and Arend Hintze).
A few weeks ago I blogged a bit about a k-mer filtering system, khmer, that we were using to reduce metagenomic data to a more tractable size by throwing out error-prone reads (see A memory efficient way to remote …
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Course page at: http://ged.msu.edu/courses/2010-fall-cse-891/:
This course will introduce biologists to computational thinking, practical computational techniques, and research topics in computational evolution. The course will consist of three intensive hands-on 5-week modules: computational competence in UNIX; data mining and hypothesis generation using the Avida digital life …read more
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(This project is a collaboration with Jason Pell and Adina Howe)
A few weeks ago I posted about a k-mer filtering approach that we were using to remove low-abundance k-mers from metagenomic data sets, prior to assembly. This technique is working well, and we've managed to do some assembly of …
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The Terabase Metagenomics meeting was good fun, but I most valued the computational component (because that's what I do). Rachel Mackelprang and Rob Knight and I wrote down a list of the computational issues involved in a petabase metagenomics project, and that list will help direct my future research. I'll …
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