Biomedical Engineering Reference
In-Depth Information
graphical view of the BLAST alignments that can be used in report
generation applications;
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EMBOSS [12] - this is a freely available suite of bioinformatics
applications and libraries and is an acronym for European Molecular
Biology Open Software Suite. The EMBOSS package contains around
150 programs covering a variety of applications such as sequence
alignment, protein domain analysis and nucleotide sequence pattern
analysis, for example, to locate repeats or CpG islands;
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Databases - a relational database provides the backend to many
applications, storing data from many sources. There are options
available when choosing a suitable relation database system. These
can be free and open source such as MySQL [13], PostgreSQL [14]
and Firebird [15], or licence-driven products such as Oracle [16] and
SQL Server [17]. We have chosen to use MySQL, primarily on the
basis that it is the system we have most knowledge of so database
administration is more straightforward. A strong secondary
consideration was that it is free of charge. Also, the requirements for
our database were relatively simple so pretty much any product would
have been suitable.
10.7.6 Next-generation sequencing
At OGT we have compiled a pipeline capable of processing data from
next-generation sequencers. The pipeline takes in the raw data reads
and runs a series of quality control checks before assembling the
reads against a reference human sequence. This is followed by a local
re-alignment to correct alignment errors due to insertions/deletions
(indels) and re-calibration of quality scores. The data are now ready for
annotation of SNPs and indels as well as interpretation of their effects.
This is a comprehensive and thorough pipeline, which makes use of a
series of FLOSS utilities.
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FastQC [18] - FastQC aims to provide a simple way to do some
quality control checks on raw sequence data coming from high-
throughput sequencing pipelines. It provides a modular set of analyses,
which you can use to give a quick impression of whether your data has
any problems before doing any further analysis;
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Burrows-Wheeler Aligner (BWA)[19] - BWA is an effi cient program
that aligns the relatively short nucleotide sequences against the long
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