Automated finishing with autofinish.

By David Gordon, C. Desmarais, P. Green. Genome Research, 2001

371 citations recorded by the source corpus.

Currently, the genome sequencing community is producing shotgun sequence data at a very high rate, but finishing (collecting additional directed sequence data to close gaps and improve the quality of the data) is not matching that rate. One reason for the difference is that shotgun sequencing is highly automated but finishing is not: Most finishing decisions, such as which directed reads to obtain and which specialized sequencing techniques to use, are made by people. If finishing rates are to increase to match shotgun sequencing rates, most finishing decisions also must be automated. The Autofinish computer program (which is part of the computer software package) does this by automatically choosing finishing reads. Autofinish is able to suggest most finishing reads required for completion of each sequencing project, greatly reducing the amount of human attention needed. sometimes completely finishes the project, with no human decisions required. It cannot solve the most complex problems, so we recommend that Autofinish be allowed to suggest reads for the first three rounds of finishing, and if the project still is not finished completely, a human finisher complete the work. We compared this Autofinish-Hybrid method of finishing against a human finisher in five different projects with a variety of shotgun depths by finishing each project twice--once with each method. This comparison shows that the Autofinish-Hybrid method saves many hours over a human finisher alone, while using roughly the same number and type of reads and closing gaps at roughly the same rate. Autofinish currently is in production use at several large sequencing centers. It is designed to be adaptable to the finishing strategy of the lab--it can finish using some or all of the following: resequencing reads, reverses, custom primer walks on either subclone templates or whole clone templates, PCR, or minilibraries. Autofinish has been used for finishing cDNA, genomic clones, and whole bacterial genomes (see http://www.phrap.org).

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d9104ab2b53699cb49f671031472907a12c5b9d3

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Citations in the corpus

A tale of two clades: monkeypox viruses. (2005, methodology): “Chromatogram data were assembled using Seqmerge (Wisconsin Package version 10.3; Accelrys), Phred/Phrap base-calling and assembly software (Ewing et al., 1998; Ewing & Green, 1998) and Consed (Gordon et al., 2001) for sequence editing.”
Multiple sequence alignment using partial order graphs (2002, methodology): “Many MSA methods have been developed with different advantages and disadvantages (Taylor, 1986; Barton and Sternberg, 1987; Altschul, 1989; Lipman et al., 1989; Subbiah and Harrison, 1989; Gotoh, 1993, 1996; Thompson et al., 1994; Notredame et al., 2000; Gordon et al., 2001), but globally optimal al”
Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial (2006, methodology): “Sequence reads were assembled using the Phred, Phrap, and Consed tools [37-39].”
The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome (2008, background): “These results are consistent with the utilization pathway reconstructed from the genome sequence, as the 9-carbon carbohydrate backbone of N-acetyl-[2-13C]neuraminic acid was metabolized into 3-carbon [2-13]pyruvate, plus unlabeled N-acetylmannosamine (ManNAc).”