Abstract:
:CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the merits of both approaches. Like the "clone by clone" method, one key challenge for this strategy was to select a low-redundancy clone set that covered the whole genome while the sequencing is in progress. The CLONEPICKER pipeline met this challenge using restriction enzyme fingerprint data, BAC end sequence data, and sequences generated from individual BAC clones as well as WGS reads. In the RGSP, an average of 7.5 clones was identified from each side of a seed clone, and the minimal overlapping clones were reliably selected. Combined with the assembled BAC fingerprint map, a set of BAC clones that covered >97% of the genome was identified and used in the RGSP.
journal_name
Genome Resjournal_title
Genome researchauthors
Chen R,Sodergren E,Weinstock GM,Gibbs RAdoi
10.1101/gr.2171704subject
Has Abstractpub_date
2004-04-01 00:00:00pages
679-84issue
4eissn
1088-9051issn
1549-5469pii
14/4/679journal_volume
14pub_type
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