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BioUtils Perl Library

Perl is a popular develop language for bioinformatics. One of the major advantages of Perl is the large collection of public libraries including a bioinformatics library called BioPerl. BioPerl encapsulates a large number of modules for common bioinformatics use such as sequence analysis and is extremely useful. However, as the BioPerl project has grown it has become somewhat convoluted in its object hierarchy which can cause significant overhead in memory usage and runtime. As high-throughput sequencing projects continue to grow in scale the extra overhead of BioPerl can become more and more problematic.

To address this in my research I have begun developing a BioUtils Perl library which contains only the bare necessities in terms of objects and data. This library can be used as a faster and more memory efficient alternative to BioPerl. However, the features implemented in this BioUtils are much more basic than BioPerl.

It currently has modules for storing DNA sequences, FASTA/Q file IO, a simple algorithm for building a consensus sequence from a set of FASTQ sequences, and a script for QC of FASTA/Q sequences.

For more detail see the [Description] page.

[Installation] instructions

Project Admins:

• Scott Yourstone