Category Archives: Uncategorized

SoCal Hackathon 2019

We are pleased to announce the second installment of the SoCal Bioinformatics Hackathon.

From 9-11 January, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University!  We are going to put a few hundred thousand metagenomic datasets on cloud infrastructure and identify known, taxonomically definable and novel viruses!  We’re specifically looking for folks who have experience in Computational Virus Hunting or Adjacent Fields! If this describes you, please apply! This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).

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C++11 on CentOS 6

CentOS is great because it is secure, but not great because it doesn’t have the latest software. Here is how to install C++11 on CentOS6 or CentOS7, and temporarily activate it in a shell. This does not change the default compiler and should cause less problems with your system (but that is not a money back guarantee … you are own your own if it does!)

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2015 SDSU Metagenomics Workshop

The 2015 SDSU Metagenomics Workshop is designed to be a combination of lectures, discussions, and practical hands on experience to bring people up to date on data analysis for metagenomics.

The workshop is being held in Adams Humanities Room 2108 from 10 am – 6 pm every day from June 22nd – 26th, 2015.

Registration is closed.

The agenda is online here, and will be updated as we progress.

We will use a VirtualBox virtual machine during the class. More information about the image and how to download is here. (Please note, the image is still subject to change, and so don’t download it yet!)

fastq to fasta

We often have people ask us how to convert fastq files to fasta format. We have a variety of code on this website, but sometimes that is not easy enough.

Here are a couple of ways to do it on the command line: using a PERL script written by Basusing the command line, or using prinseq-lite. Here is a C++ version that you can compile (e.g. with c++ -o fastq2fasta fastq2fasta.cpp) and run on your machine.

We also have a simple form that converts fastq files to fasta files (DNA only … it does not give you the quality scores).