The Bio Library

Overview

This library has been developed over the last few years, and has been used in a number of applications.

It contains functionality for working with sequences and alignments, including reading and writing many formats.

Functionality

Sequence formats supported: Fasta, FastQ (Illumina and Sanger), 2bit, SFF, ACE.

Supported alignment formats: ACE, BlastXML, PSL (Blat), Bowtie, Soap, GFF3, BED.

Other formats: OBO ontology files, GOA gene associations.

Algorithms: clustering, sequence alignments.

Examples

Starting with version 0.5, there is an /examples directory, where you will find some simple applications, illustrating how to use various functionality.

Where you can help

This library is in maintenance mode, which means no new functionality will be added beyond bug fixes, and its functionality will gradually be migrated out into smaller, more specialized libraries that use the biocore library.

If you find you need some of the functionality, you might want to consider factoring it out, and wrapping it up as a separate library.

No new development will take place here, and functionality will gradually be ported from this library and rolled out as several smaller libraries, based on biocore.