DNA sequence quality trimming and vector removal

By Hui-Hsien Chou, Michael H. Holmes. Bioinform., 2001

569 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c8e74e889236808484b61ad23381aab1331c7abd

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Citations in the corpus

Minimus: a fast, lightweight genome assembler (2007, methodology): “For the other data-sets (zebrafish gene and mouse BACs) we followed the protocol described at [30], specifically we used the program Lucy [31] for quality trimming, followed by a k-mer based vector trimming protocol.”
Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem (2017, methodology): “Quality control for 454 shotgun sequences was carried out by the LUCY program (Chou and Holmes, 2001) with minimum quality score of 21 and maximum error rate of 0.01, resulting in 17,096,024 high quality sequences.”
Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities (2010, methodology): “Obtained sequencing reads were quality trimmed using the software tool “lucy” [11] to an accuracy of 99.”
Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. (2012, methodology): “The sequence reads were vector and quality trimmed with Lucy version 1.19p (Chou and Holmes 2001), resulting in 138,989 reads, which were screened for contamination with rice plant DNA using megablast against the O. sativa genome (98% i.d., min e-30).”
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. (2009, methodology): “Only when the LUCY end-trimming stringency was increased to ≤0.2% per base error probability (equivalent to a phred quality score of ≥27), combined with clustering at ≤97% identity, did the number of OTUs approach the expected number of E. coli MG1655 rRNA operons.”
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data (2006, methodology): “Trimming and vector removal are then done using TIGR’s Lucy (7).”
Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene (2011, methodology): “Sequences were trimmed using Lucy ( Chou and Holmes 2001 )o n the basis of Phred quality scores (Ewing et al. 1998; Ewing and Green 1998).”
A Bioinformatician's Guide to Metagenomics (2008, unknown): “Another vectortrimming tool, LUCY, avoids this problem by specifying error rates as a function of sequence position.”