Lucy pipeline

Lucy specifications


Unique identifier OMICS_14823
Name Lucy
Alternative name Lucy2
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A gene sequence.
Input format FASTA
Output data A view of the sequence with low-quality regions in gray text and vector regions found in white text.
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.20
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Hui-Hsien Chou <>

Publications for Lucy

Lucy IN pipelines

PMCID: 5716196
PMID: 29036322
DOI: 10.1093/nar/gkx853

[…] of 10 bp and sequences beyond the last window with average quality value less than the specified threshold were truncated. the trimming parameters were as referred to in the trimming software, lucy (23,24)., cleaned reads were aligned to the b73 reference genome (agp v2) (25) using gsnap (26). only confidently mapped reads were used for subsequent analyses, which are uniquely mapped […]

PMCID: 4047050
PMID: 24901369
DOI: 10.1371/journal.pone.0098870

[…] the new transcriptome data with gs de novo assembler v2.3 (‘newbler’; 454 life sciences/roche, indianapolis, in, usa) to create a cdna de novo assembly with default threshold options. we used lucy [24] to trim low quality nucleotide reads and deleted any assembled contigs below 100 nucleotides in length. we found sequences similar to opsin using blastp similarity searches [25]. […]

PMCID: 3667073
PMID: 23734264
DOI: 10.1371/journal.pone.0065902

[…] on a roche gs-flx sequencer. the adaptors, low-complexity sequences, sequences with an excess of errors (more than 4% of n) and very short sequences (less than 100 bp) were trimmed by using the lucy [31] and seqclean ( the duplicated reads were eliminated by using cd-hit-454 software [32]. the pre-processed sequences were then subject to assembling […]

PMCID: 4972453
PMID: 23665961
DOI: 10.1038/nature12132

[…] 454, sanger and miseq reads were assembled using newbler version 2.6 de novo genome assembler (with the -scaffold option). vector and poor quality regions were masked in the sanger reads using the lucy2 software. natural and artificial duplicates in pyrosequencing reads were eliminated using the cd-hit pipeline. the miseq read pairs (2×250) were merged and adaptor-trimmed with seqprep using […]

PMCID: 3409161
PMID: 22860121
DOI: 10.1371/journal.pone.0042388

[…] and 5′ end of the polylinker) was used for the 5′ end sequencing and the t7 (reverse) primer was used for the 3′ end., base calls were performed with phred [50], trace and vector clipping with lucy [51], and low complexity regions detected and masked using repeatmasker ( traces were mapped to the mouse mm36 ncbi reference sequence (april 2006), chromosome […]

Lucy institution(s)
Department of Computer Science, Iowa State University, Ames, IA, USA; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
Lucy funding source(s)
This project is supported by the NIH grant 4R33GM066400.

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