github.com/kortschak/biogo

bíogo

Installation

    $ go get github.com/biogo/biogo/...

Overview

bíogo is a bioinformatics library for the Go language.

Getting help

Help or similar requests are preferred on the biogo-user Google Group.

https://groups.google.com/forum/#!forum/biogo-user

Contributing

If you find any bugs, feel free to file an issue on the github issue tracker. Pull requests are welcome, though if they involve changes to API or addition of features, please first open a discussion at the biogo-dev Google Group.

https://groups.google.com/forum/#!forum/biogo-dev

Citing

If you use bíogo, please cite Kortschak, Snyder, Maragkakis and Adelson "bíogo: a simple high-performance bioinformatics toolkit for the Go language", doi:10.21105/joss.00167, and Kortschak and Adelson "bíogo: a simple high-performance bioinformatics toolkit for the Go language", doi:10.1101/005033.

The Purpose of bíogo

bíogo stems from the need to address the size and structure of modern genomic and metagenomic data sets. These properties enforce requirements on the libraries and languages used for analysis:

• speed - size of data sets
• concurrency - problems often embarrassingly parallelisable

In addition to the computational burden of massive data set sizes in modern genomics there is an increasing need for complex pipelines to resolve questions in tightening problem space and also a developing need to be able to develop new algorithms to allow novel approaches to interesting questions. These issues suggest the need for a simplicity in syntax to facilitate:

• ease of coding
• checking for correctness in development and particularly in peer review

Related to the second issue is the reluctance of some researchers to release code because of quality concerns.

The issue of code release is the first of the principles formalised in the Science Code Manifesto.

Code  All source code written specifically to process data for a published
      paper must be available to the reviewers and readers of the paper.

A language with a simple, yet expressive, syntax should facilitate development of higher quality code and thus help reduce this barrier to research code release.

Articles

bíogo: a simple high-performance bioinformatics toolkit for the Go language

Analysis of Illumina sequencing data using bíogo

Using and extending types in bíogo

Yet Another Bioinformatics Library

It seems that nearly every language has it own bioinformatics library, some of which are very mature, for example BioPerl and BioPython. Why add another one?

The different libraries excel in different fields, acting as scripting glue for applications in a pipeline (much of [1, 2, 3]) and interacting with external hosts [1, 2, 4, 5], wrapping lower level high performance languages with more user friendly syntax [1, 2, 3, 4] or providing bioinformatics functions for high performance languages [5, 6].

The intended niche for bíogo lies somewhere between the scripting libraries and high performance language libraries in being easy to use for both small and large projects while having reasonable performance with computationally intensive tasks.

The intent is to reduce the level of investment required to develop new research software for computationally intensive tasks.

1. BioPerl http://genome.cshlp.org/content/12/10/1611.full http://www.springerlink.com/content/pp72033m171568p2

2. BioPython http://bioinformatics.oxfordjournals.org/content/25/11/1422

3. BioRuby http://bioinformatics.oxfordjournals.org/content/26/20/2617

4. PyCogent http://genomebiology.com/2007/8/8/R171

5. BioJava http://bioinformatics.oxfordjournals.org/content/24/18/2096

6. SeqAn http://www.biomedcentral.com/1471-2105/9/11

Library Structure and Coding Style

The bíogo library structure is influenced both by the Go core library.

The coding style should be aligned with normal Go idioms as represented in the Go core libraries.

Quality Scores

Quality scores are supported for all sequence types, including protein. Phred and Solexa scoring systems are able to be read from files, however internal representation of quality scores is with Phred, so there will be precision loss in conversion. A Solexa quality score type is provided for use where this will be a problem.

Copyright and License

Copyright ©2011-2013 The bíogo Authors except where otherwise noted. All rights reserved. Use of this source code is governed by a BSD-style license that can be found in the LICENSE file.

The bíogo logo is derived from Bitstream Charter, Copyright ©1989-1992 Bitstream Inc., Cambridge, MA.

BITSTREAM CHARTER is a registered trademark of Bitstream Inc.