Trimming procedures are an important part of the sequence analysis pipeline in an EST Sequencing Project. In general, trimming is done in several phases, each one detecting and removing some kind of undesirable artifact, such as low quality sequence, vectors or adapters, and contamination. However, this strategy often results in a phase being unable to recognize its target because part of it was removed during a previous phase. To remedy this drawback, we propose a new strategy, where each phase detects but does not remove its target, leaving this decision to a post processing step occurring after all phases. Our tests show that this strategy can significantly improve the detection of artifacts. © Springer-Verlag Berlin Heidelberg 2005.3594 206209Baudet, C., Dias, Z., New EST trimming strategy (2005) Technical Report, IC-05-09. , Institute of Computing - University of Campinas, May(2005) Cattle EST Project, , http://titan.biotec.uiuc.edu/cattle/cattle_project.htm, The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, JanuaryChou, H., Hohnes, M.H., DNA sequence quality trimming and vector removal (2001) Bioinformatics, 17, pp. 1093-1104Green, P., (2004) Phrap Homepage: Phred, Phrap, Consed, Swat, Cross_match and Repeat-masker Documentation, , http://www.phrap.org, MarchScheetz, T.E., Trivedi, N., Roberts, C.A., Kucaba, T., Berger, B., Robinson, N.L., Birkett, C.L., Casavant, T.L., ESTprep: Preprocessing cDNA sequence (2003) Bioinformatics, 19 (11), pp. 1318-1324. , NovemberTelles, G.P., Da Silva, F.R., Trimming and clustering sugarcane ESTs (2001) Genetics and Molecular Biology, 24 (1-4), pp. 17-23. , December