Lucy protocols

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Lucy specifications

Information


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 http://lucy.sourceforge.net/
Maintained Yes

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Maintainer


  • person_outline Hui-Hsien Chou <>

Publications for Lucy

Lucy in pipelines

 (30)
2017
PMCID: 5751233
PMID: 29210992
DOI: 10.3390/ijms18122630

[…] switzerland), and the raw data were processed with the roche gs flx software (version 2.5.3, 454 life sciences, roche, basel, switzerland) at quality score threshold 40 and quality-trimmed with lucy software (version 2.19; available online: http://lucy.sourceforge.net/) [] and seqclean (version 1.0; available online: http://compbio.dfci.harvard.edu). the resulting sequence reads […]

2016
PMCID: 5108929
PMID: 27895627
DOI: 10.3389/fmicb.2016.01790

[…] inherent artifacts removal using cd-hit-454 (version 4.5.4, default parameter, and 98% of identity option) () and filtered by quality (phred quality -q = or > 20) and length (>100 bp) using lucy program (version 1.2) (). results of sequencing basic statistics are listed in table . the metagenome sequencing data has been deposited at genbank under the biosample accession number […]

2015
PMCID: 4419794
PMID: 25762217
DOI: 10.1093/gbe/evv047

[…] using an applied biosystems 3730xl dna analyzer. base calling was performed using tracetuner 3.0.4 beta () to obtain fasta and quality values. vector and quality trimming were performed using lucy 1.19p (). only 96 reads were retained after trimming. mapping reads was performed using smalt 0.7.3 (http://www.sanger.ac.uk/resources/software/smalt/, last accessed march 23, 2015) resulting […]

2015
PMCID: 4557894
PMID: 26329285
DOI: 10.1186/s12864-015-1870-0

[…] ca., expressed sequence tags (ests) were cleaned and assembled with an automated pipeline (est2uni) [], which includes base calling (phred), vector trimming and low quality bases removal with lucy [], and repeat masking with repeatmasker-open 3.0 []. afterwards, the assembly of sequencing reads into unique consensus sequences (unigenes) [] was conducted with cap3 [], and functional […]

2014
PMCID: 4224446
PMID: 25379700
DOI: 10.1371/journal.pone.0112223

[…] raw data from 454 sequencing were pre-processed to remove adaptor-ligated regions, primers and very short sequences (<50 bp) by seqclean (v86_64) and to trim low-quality regions by the lucy program (v2.19) . cleaned and qualified reads were then assembled de novo in newbler (v2.5.3) with optimal parameters , , . the assembled unique sequences were separately combined and clustered […]


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Lucy in publications

 (112)
PMCID: 5727146
PMID: 29052098
DOI: 10.1007/s11103-017-0663-z

[…] variants), which were grouped into isogroups (equivalent to genes). additionally, raw reads that were not assembled into isotigs or contigs were remained as singletons and preprocessed using the lucy dna sequence quality and vector trimming tool (chou and holmes ). after removing short singletons less than 200 bp, redundant singletons were filtered out using the cd-hit-est program […]

PMCID: 5623005
PMID: 29018358
DOI: 10.3389/fphys.2017.00735

[…] the min elute gel recovery kit (qiagen, valencia, ca, usa) and sequenced using the proton i chip of ion proton™ system (life technology, thermo scientific, wilmington, de, usa). using the tagdust, lucy, and seqclean software programs with default parameters, short or low-quality sequences and adaptor sequences were removed (li and chou, ; chen et al., ; lassmann et al., ). male and female […]

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 (,)., cleaned reads were aligned to the b73 reference genome (agp v2) () using gsnap (). only confidently mapped reads were used for subsequent analyses, which are uniquely mapped with at least […]

PMCID: 5515459
PMID: 28719637
DOI: 10.1371/journal.pone.0181503

[…] sequence analysis and assembly were based in newbler assembler v.2.5.3. inherent artifacts, replicates or low quality sequences were further filtered and removed with replicates software [] and lucy program []., two approaches were used to analyze the taxonomic distribution of each read hit. first, mg-rast server [] using the lowest common ancestor (lca) method and megan4 [], […]

PMCID: 5529022
PMID: 28708894
DOI: 10.1371/journal.pntd.0005778

[…] was homogenized in 1 ml of 3% trichloroacetic acid and centrifuged at 4,000 g, 4°c, 20 min. the ph of the supernatant was adjusted to 7.4 with 1 m tris. the atp concentration was measured on anthos lucy2 (asys hitech gmbh, austria) using the adenosine 5′-triphosphate (atp) bioluminescent assay kit (sigma-aldrich, st. louis, mo)., 30 mg of liver tissue (two pieces for each animal) […]


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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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