Genome Res 1998 Mar;8(3):195-202
Department of Molecular Biotechnology, University of
Washington, Seattle, Washington 98195-7730, USA.
Sequencing of large clones or small genomes is generally done
by the shotgun approach (Anderson et al. 1982). This has two
phases: (1) a shotgun phase in which a number of reads are
generated from random subclones and assembled into contigs,
followed by (2) a directed, or finishing phase in which the
assembly is inspected for correctness and for various kinds of
data anomalies (such as contaminant reads, unremoved vector
sequence, and chimeric or deleted reads), additional data are
collected to close gaps and resolve low quality regions, and
editing is performed to correct assembly or base-calling errors.
Finishing is currently a bottleneck in large-scale sequencing
efforts, and throughput gains will depend both on reducing the
need for human intervention and making it as efficient as
possible. We have developed a finishing tool, consed, which
attempts to implement these principles. A distinguishing feature
relative to other programs is the use of error probabilities from
our programs phred and phrap as an objective criterion to guide
the entire finishing process. More information is available at
http:// www.genome.washington.edu/consed/consed. html.
PMID: 9521923, UI: 98190161