SeqtrimNEXT pipeline

SeqtrimNEXT specifications

Information


Unique identifier OMICS_01093
Name SeqtrimNEXT
Alternative name SeqTrim
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA,PHD
Output format FASTA,TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes

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Maintainer


  • person_outline Gonzalo Claros <>

Information


Unique identifier OMICS_01093
Name SeqtrimNEXT
Alternative name SeqTrim
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input format FASTA,PHD
Output format FASTA,TXT
Programming languages Javascript
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Gonzalo Claros <>

Publication for SeqtrimNEXT

SeqtrimNEXT IN pipelines

 (2)
2015
PMCID: 4468178
PMID: 26090306
DOI: 10.1186/s40064-015-1062-z

[…] the enrichment of the sample in molecules flanked by a different adaptor. the second pcr products were sent for dna pyrosequencing by 454 flx method (roche) at lifesequencing sl (valencia, spain)., seqtrim software was used to clean sequences and to remove adaptor sequences and pcr artifacts (falgueras et al. 2010). the resulting sequences were assembled into contigs by cap3 (huang and madan […]

2011
PMCID: 3175227
PMID: 21854637
DOI: 10.1186/1471-2164-12-424

[…] and whole genome sequences derived from roche 454 sequencing of 3-kb, 8-kb and 20-kb paired-end libraries (unpublished). raw bess were filtered and trimmed for quality and vector contamination using seqtrim [65]. only bess that had > 98% identity to the query for over 80% of their length were considered. in cases in which the bess were paired (when both 5' and 3' ends of the same bac insert […]

SeqtrimNEXT institution(s)
Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, Málaga, Spain; Plataforma Andaluza de Bioinformática, Universidad de Málaga, Málaga, Spain; Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain; Departamento de Arquitectura de Computadores, Universidad de Málaga, Málaga, Spain
SeqtrimNEXT funding source(s)
Supported by the Spanish MICINN grants AGL2009-12139-C02-02 and BIO2009-07490, the European Union grant PLE2009-0016, and Junta de Andalucía funding to the research groups BIO-114 and TIC-113.

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