In:
Genome Research, Cold Spring Harbor Laboratory, Vol. 12, No. 5 ( 2002-05-01), p. 824-831
Abstract:
We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4× to 6×, despite having up to 42.2% in exact repeats. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Green and A.F. Smit.]
Type of Medium:
Online Resource
ISSN:
1088-9051
,
1549-5469
Language:
English
Publisher:
Cold Spring Harbor Laboratory
Publication Date:
2002
detail.hit.zdb_id:
1483456-X
SSG:
12
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