A forward–reverse constraint is often produced by sequencing of both ends of a subclone. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward–reverse constraints.Īn unusual feature of CAP3 is the use of forward–reverse constraints in the construction of contigs. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. Results of CAP3 on four BAC data sets are presented. Forward–reverse constraints are used to correct assembly errors and link contigs. Efficient algorithms are employed to identify and compute overlaps between reads. 1998) are used in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. Base quality values produced by PHRED ( Ewing et al. A capability to clip 5′ and 3′ low-quality regions of reads is included in the CAP3 program. The CAP3 program includes a number of improvements and new features. We have developed the third generation of the CAP sequence assembly program ( Huang 1992). Continued development and improvement of sequence assembly programs are required to meet the challenges of the human, mouse, and maize genome projects. TIGR Assembler has been used in a number of megabase microbial genome projects ( Sutton et al. The PHRAP program clips 5′ and 3′ low-quality regions of reads and uses base quality values in evaluation of overlaps and generation of contig sequences ( Green 1996). The GAP4 program has a number of useful interactive features ( Bonfield et al. The FAKII program provides a library of routines for each phase of the assembly process ( Larson et al. 1994 Kececioglu and Myers 1995 Sutton et al. 1993 Gleizes and Henaut 1994 Lawrence et al. A number of DNA sequence assembly programs have been developed ( Staden 1980 Peltola et al. A major phase in this strategy is to assemble short reads into long sequences. The shotgun sequencing strategy has been used widely in genome sequencing projects.
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