SeqtrimNEXT statistics

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Protocols

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

Versioning


No version available

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 citations

 (14)
call_split

Glutamate synthases from conifers: gene structure and phylogenetic studies

2018
BMC Genomics
PMCID: 5775586
PMID: 29351733
DOI: 10.1186/s12864-018-4454-y
call_split See protocol

[…] The sequences obtained using the FLX-454 system were processed by the UMA Bioinformatics Platform using two tools: SeqTrimNext pipeline (http://scbi.uma.es/seqtrimnext) [] for sequence preprocessing and MIRA 3 [] for assembly.The scaffold containing the P. taeda Fd-GOGAT gene sequence was obtained from NCBI (http: […]

library_books

An approach to forecast human cancer by profiling microRNA expressions from NGS data

2017
BMC Cancer
PMCID: 5267436
PMID: 28122525
DOI: 10.1186/s12885-016-3042-2

[…] e 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 [], AdapterRe […]

call_split

De novo Analysis of the Epiphytic Transcriptome of the Cucurbit Powdery Mildew Fungus Podosphaera xanthii and Identification of Candidate Secreted Effector Proteins

2016
PLoS One
PMCID: 5053433
PMID: 27711117
DOI: 10.1371/journal.pone.0163379
call_split See protocol

[…] 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 sequ […]

call_split

Patterns of Transcript Abundance of Eukaryotic Biogeochemically Relevant Genes in the Amazon River Plume

2016
PLoS One
PMCID: 5012681
PMID: 27598790
DOI: 10.1371/journal.pone.0160929
call_split See protocol

[…] 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 r […]

call_split

Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

2016
PLoS One
PMCID: 4712138
PMID: 26731732
DOI: 10.1371/journal.pone.0142759
call_split See protocol

[…] automated Perl pipeline was created. Raw reads were sorted by primer sequences for the ITS, LSU, and rbcL markers using AGREP version 2.04 allowing 1 mismatch. Sorted reads were quality-trimmed using SeqTrim [] with a 10 bp sliding window, excluding windows with an average Phred score less than 20, and removing reads less than 80 bp after trimming.Quality-trimmed reads were sorted by average read […]

library_books

Transcriptome wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats

2015
BMC Genomics
PMCID: 4636790
PMID: 26545587
DOI: 10.1186/s12864-015-2177-x

[…] llumina’s OLB version 1.9. A total of 113.7; 137.2; 125.3 and 190.6 millions of reads were obtained for the T3, T6, L6 and L7 samples, respectively.The resulting reads were trimmed and analyzed using SeqTrimNext software []. Only the pairs in which both reads passed the quality test were further analyzed. After read trimming, a total of 110.4, 128.7, 121 and 180.5 millions of paired-end reads were […]

Citations

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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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