ABBA

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ABBA: Assembly Boosted By Amino acid sequences

Overview

Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. See the journal paper.

For additional information on short read assembly check the following University of Maryland CBCB web sites:


Documentation

Documentation on running ABBA is included in the tarball here: ftp://ftp.cbcb.umd.edu/pub/data/dsommer


"NOTE: ABBA relies on other tools in the AMOS package, so you need to download and install AMOS as well."

References

Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads.

Salzberg SL, Sommer DD, Puiu D, Lee VT 2008 PLoS Computational Biology 4(9): e1000186 doi:10.1371/journal.pcbi.1000186


Acknowledgements

The development of ABBA was supported by the National Institutes of Health under grants R01-LM06845 and R01-LM007938 to SLS.