boalang / NR

Detecting and correcting misclassified sequences in the large-scale public databases

Detecting and correcting misclassified sequences in the large-scale public databases

Dataset: Non Redundant (NR) and CD-HIT clustering information

• Protobuffer schema and the step by step data generation is shown here.
• JSON files version of NR for MongoDB

Detected taxonomically misclassified sequences

Detected misclassification in the clusters

Correcting misclassified sequences

Experiments

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Boa_g: Boa for genomics

Boa_g is a domain-specific language and infrastructure on top of Hadoop for genomics data. Website: https://boalang.github.io/bio/

Boa_g example on the infrastructure: http://boa.cs.iastate.edu/examples/boag/index.php

Prerequisites

You need to install Java. Boa_g compiler is written in Java. It can be downloaded here.

Run Boa_g

These instructions will get you a command line, jupyter notebook, Docker container, and Hadoop version of Boa_g. You can also set up a programming environment in Eclipse.

From Jupyter notebook

• Prerequisite is Jupyter: install
• Jupyter notebook instructions and example

From command line

• Instructions on How to run Boa_g scripts on a command line

On a Docker container

• Instructions on How to run Boa_g scripts in a Docker container

On Hadoop

• Instructions on how to run Boa_g on Bridges

Boa_g Compiler source code

• Boa_g compiler is written in Java. See the source code
• This is a video on step by step instructions to set up programming environment on Eclipse for Boa compiler. link

Boa_g Query Script examples:

• Query over NR database

Download dataset and VirtualBox

• Google Drive Link
• Web interface is also implemented in the Ubuntu linux and it can be seen in the VirtualBox.