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KMID : 1132720090070010046
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Genomics & Informatics
2009 Volume.7 No. 1 p.46 ~ p.48
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A Simple Java Sequence Alignment Editing Tool for Resolving Complex Repeat Regions
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Ham Seong-Il
Lee Kyung-Eun
Park Hyun-Seok
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Abstract
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Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.
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KEYWORD
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fragment assembly, genome sequencing, whole genome fragment assembly
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