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Assembly of fingerprint contigs: parallelized FPC.

S R Ness¹, W Terpstra, M Krzywinski

¹Genome Sequence Centre, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada.

Bioinformatics (Oxford, England)

|April 6, 2002

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We enhanced the FingerPrint Contigs (FPC) program for parallel processing to speed up the assembly of large genomic clone fingerprint databases. This optimized FPC accelerates contig assembly for complex genomic projects.

Area of Science:

Genomics
Bioinformatics

Background:

FingerPrint Contigs (FPC) is commonly used for assembling genomic clone fingerprints into contigs.
Large-scale genomic projects generate substantial fingerprint data, necessitating efficient assembly methods.

Purpose of the Study:

To enhance the FingerPrint Contigs (FPC) program for parallel processing.
To improve the rate of contig assembly from large fingerprint databases.

Main Methods:

Adapted the FPC program to run in parallel across multiple processors and servers.
Applied the parallelized FPC to assemble large mammalian BAC fingerprint databases.

Main Results:

The parallelized FPC significantly improves the speed of contig assembly.

Related Experiment Videos

Successfully assembled mammalian BAC fingerprint databases exceeding 300,000 fingerprints.

Conclusions:

Parallelized FPC offers a scalable solution for assembling large genomic fingerprint datasets.
This adaptation enhances the efficiency of contig assembly in genomics research.