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Protocols

Figaro specifications

Information


Unique identifier OMICS_14822
Name Figaro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl
License Artistic License version 2.0
Computer skills Advanced
Version 1.05
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Mihai Pop

Publication for Figaro

Figaro citations

 (8)
library_books

Reconstruction of the microalga Nannochloropsis salina genome scale metabolic model with applications to lipid production

2017
BMC Syst Biol
PMCID: 5496344
PMID: 28676050
DOI: 10.1186/s12918-017-0441-1

[…] e divided this process in 4 steps: (1) Illumina raw data was error corrected, and then sequences were assembled using the Trinity package. (2) Roche 454 GS FLX raw reads were cleaned and trimmed with Figaro []. (3) Using BLASTN, 454 reads were mapped to Illumina contigs in order to avoid redundancy between corrected Illumina contigs and 454 data. (4) We generated 3 sets of data: The first was cons […]

library_books

High Phylogenetic Diversity of Glycosyl Hydrolase Family 10 and 11 Xylanases in the Sediment of Lake Dabusu in China

2014
PLoS One
PMCID: 4231106
PMID: 25392912
DOI: 10.1371/journal.pone.0112798

[…] By using the Figaro software (http://sourceforge.net/apps/mediawiki/amos/index.php?title=Figaro), vector sequences introduced by automated Sanger sequencing machines were removed. The sequences were analyzed by N […]

library_books

A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences

2013
Bioinform Biol Insights
PMCID: 3583267
PMID: 23585714
DOI: 10.4137/BBI.S11064

[…] Sanger reads, quality values, and ancillary information of C. remanei were downloaded from the NCBI Trace Archive FTP site (ftp://ftp.ncbi.nih.gov/pub/TraceDB). Reads were trimmed with the Figaro_ trim_seqs utility of the Figaro package using the vector clipping information provided by the Trace Archive. Illumina reads of C. angaria were downloaded from the NCBI Sequence Read Archive FT […]

library_books

ESTclean: a cleaning tool for next gen transcriptome shotgun sequencing

2012
BMC Bioinformatics
PMCID: 3630001
PMID: 23009593
DOI: 10.1186/1471-2105-13-247

[…] ses and removing contamination has become one of the most important steps. To remove contamination, several software tools are available, including VecScreen [], Lucy [], Cross_match [], SeqClean [], Figaro [], and SeqTrim []. Although these programs have been used in many sequencing projects, most of them are not appropriate to detect the diverse contamination produced by several NGS-based protoc […]

library_books

Phylogenetic Diversity and Environment Specific Distributions of Glycosyl Hydrolase Family 10 Xylanases in Geographically Distant Soils

2012
PLoS One
PMCID: 3422244
PMID: 22912883
DOI: 10.1371/journal.pone.0043480

[…] Vector sequences introduced by automated Sanger sequencing machines were removed using Figaro software (http://sourceforge.net/apps/mediawiki/amos/index.php?title=Figaro). Then the sequences were analyzed with NCBI BLASTx (version 2.2.13) against the GenBank nr database. An E-score (ex […]

call_split

A whole genome assembly of the domestic cow, Bos taurus

2009
Genome Biol
PMCID: 2688933
PMID: 19393038
DOI: 10.1186/gb-2009-10-4-r42
call_split See protocol

[…] final assembly, with previous releases occurring in 2004, 2005, and 2006. For the UMD2 assembly, no sequences other than the BCM traces were used. We trimmed the reads to remove vector sequence using Figaro [], which automatically determines vector sequence by identifying common prefixes in the reads. We trimmed the 3' end of the reads so that the mean error rate (computed from the quality scores) […]


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Figaro institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland - College Park, MD, USA; Applied Mathematics and Scientific Computation Program, University of Maryland - College Park, MD, USA; Institute for Physical Sciences and Technology, University of Maryland - College Park, MD, USA
Figaro funding source(s)
This work was supported in part by grant R01-LM006845 from NIH and grant HU001-06-1-0015 from the Uniformed Services University of the Health Sciences administered by the Henry Jackson Foundation, by NSF grant DMS 0616585 and NIH grant 1R01HG0294501, and by University of Maryland NSF VIGRE fellowship DMS0240049.

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