SeqtrimNEXT protocols

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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

 (4)
2016
PMCID: 5012681
PMID: 27598790
DOI: 10.1371/journal.pone.0160929

[…] hiseq2000, miseq, or hiseq2500 platforms (illumina inc., san diego, ca)., paired-end reads were joined using the she-ra program [] with a quality metric score of 0.5. paired reads were trimmed using seqtrim 20 []. poly(a)-rna capture methods were not 100% successful, as some rrna would remain in the sample, so the minimal (0.14–0.33%) rrna were removed in silico after sequencing. remaining rrna […]

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. ). the resulting sequences were assembled into contigs by cap3 (huang and madan ). two […]

2011
PMCID: 3156302
PMID: 21499864
DOI: 10.1007/s10142-011-0223-6

[…] primers., clones with confirmed single inserts were sequenced single-pass (mcgill university and génome québec innovation center). sequences were base called using phred (green ) and trimmed using seqtrim (falgueras et al. ). the sequences appear in public sequence databases under the genbank accession numbers gw696871 to gw698115. the 1,108 arctic and 609 temperate processed expressed […]

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 []. 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 […]


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SeqtrimNEXT in publications

 (21)
PMCID: 5796392
PMID: 29391047
DOI: 10.1186/s13567-018-0506-1

[…] analysis was performed at the andalusian platform of bioinformatics of the university of malaga. raw reads were pre-processed using the in-house developed customizable pre-processing pipeline seqtrimnext []. contaminants, sequencing adapters, short (< 17 nucleotide) and bad quality reads (phred score < 20) were removed, to ensure that only high quality sequences were used […]

PMCID: 5601413
PMID: 28955364
DOI: 10.3389/fpls.2017.01576

[…] tested in pollen, pistil and leaf tissues (carmona et al., , ). housekeeping sequences and amplicon sizes are detailed in supplementary table ., all clones sequenced were pre-processed using seqtrimnext (falgueras et al., ) as described in carmona et al. () to remove linkers, adaptors, vector fragments and contaminated sequences among others, while keeping the longest informative part […]

PMCID: 5568602
PMID: 28830520
DOI: 10.1186/s12938-017-0356-5

[…] the workflow receives as input files the raw reads and the transcriptome, both in fasta format. each file of raw reads is considered an experimental condition. raw reads are then pre-processed using seqtrimnext [] to remove noisy sequences and retain only reliable reads. useful reads are then mapped to the corresponding transcriptome using bowtie2 [] with default parameters and the −a option […]

PMCID: 5267436
PMID: 28122525
DOI: 10.1186/s12885-016-3042-2

[…] alignment algorithm, having a time complexity of o(m n). btrim [] is a very fast tool that works with a time complexity of o(m n/w), where w is word length of the computer. fastx, tagcleaner [] and seqtrim [] are useful only for single end reads. besides handling of both single and paired end reads, low quality trimming can be performed with trimomatic [], allentrimmer [], cutadapt [], […]

PMCID: 5053433
PMID: 27711117
DOI: 10.1371/journal.pone.0163379

[…] and gs flx titanium picotiterplate kit on a gs flx instrument (454 life sciences). all kits were used according to the manufacturer’s instructions., before assembly, 454 reads were pre-processed by seqtrimnext v.2.0.54 pipeline (http://www.scbi.uma.es/seqtrimnext), available at the plataforma andaluza de bioinformática (university of málaga, spain), using plugins to remove low and high size […]


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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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