SeqBuster protocols

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SeqBuster statistics

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SeqBuster specifications

Information


Unique identifier OMICS_00367
Name SeqBuster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • miraligner

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Versioning


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Documentation


Maintainers


  • person_outline Eulalia Martí <>
  • person_outline Xavier Estivill <>

Additional information


https://github.com/lpantano/seqbuster/wiki

Publications for SeqBuster

SeqBuster in pipelines

 (6)
2018
PMCID: 5887145
PMID: 29467169
DOI: 10.1534/genetics.118.300791

[…] based on sequence identity using the collapse_reads_md.pl module of mirdeep2. collapsed reads were further annotated for mirna by mapping to mirbase version 21 (; ; ) using the miraligner module of seqbuster (). isomirs were identified using the r isomirs (v1.3.0) package of seqbuster. pairwise differential expression was performed among different groups using deseq2 (v1.12.4) ()., adult […]

2017
PMCID: 5514905
PMID: 28402935
DOI: 10.18632/oncotarget.16664

[…] [] were filtered using blastn v2.2.30 []. mirna and isomirna quantification in filtered reads were performed using the quantifier.pl module from mirdeep2 v2.0.0.7 software [] and miraligner from seqbuster software [] with default parameters using precursor and mature mirna sequences as reference (mirbase v21). differential expression analyses of the size factor normalized counts of mature […]

2017
PMCID: 5629335
PMID: 28860320
DOI: 10.1534/genetics.117.300221

[…] score, the sequence of each transcript was blasted against the a. gambiae pest repeatmasker library provided by vectorbase.org. for the small rna dataset. we generated a count matrix using seqbuster and seqcluster suites (). and used deseq2 () for differential expression analysis and log2 transformation of the count data. only putative small rna loci with a mean expression of >5 […]

2017
PMCID: 5798962
PMID: 29219730
DOI: 10.1080/15476286.2017.1403003

[…] (10 alignments per read were allowed). we compiled a comprehensive annotation set from mirbase/mirgenedb [] for mirnas, pirbase/pirnabank for pirnas [], gencode [] for other rnas and trnas. we used seqbuster [] to get isomir and mirna profiles of our samples. to count the reads mapped on other rnas, htseq [] was utilized in a python script. we used a threshold of 10 median read count per sncrna […]

2016
PMCID: 4770244
PMID: 26819412
DOI: 10.1093/nar/gkw039

[…] (cpm). the ranked lists were obtained using the borda rule., to obtain a survey on mirna sequence variability in the samples, trimmed reads were processed with a pipeline containing the software seqbuster-miraligner (). seqbuster identifies different types of mirna variability that include 5′- and 3′-end modifications, 3′ addition variants and nucleotide substitution variants. the mapping […]


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SeqBuster in publications

 (13)
PMCID: 5837101
PMID: 29505615
DOI: 10.1371/journal.pone.0193527

[…] small rna libraries were prepared with the nebnext® small rna library preparation kit and sequenced in an illumina hiseq2000 platform. mirnas, isomirs and clusters of small rnas were annotated using seqbuster/seqcluster framework in 5 plasma and 10 milk samples that passed the initial quality control. the rna yield was 81 ng/ml [standard deviation (sd): 41] and 3985 ng/ml (sd: 3767) for plasma […]

PMCID: 5887145
PMID: 29467169
DOI: 10.1534/genetics.118.300791

[…] based on sequence identity using the collapse_reads_md.pl module of mirdeep2. collapsed reads were further annotated for mirna by mapping to mirbase version 21 (; ; ) using the miraligner module of seqbuster (). isomirs were identified using the r isomirs (v1.3.0) package of seqbuster. pairwise differential expression was performed among different groups using deseq2 (v1.12.4) ()., adult […]

PMCID: 5794191
PMID: 29357384
DOI: 10.1371/journal.ppat.1006802

[…] number of reads on the fc and cb mapping onto mirnas with at least 2 counts in a given sample are shown (). two independent pipelines were used for the analysis of the differential mirna expression, seqbuster [] and oasis []. both pipelines showed a high level of agreement in the detection of differentially expressed mirnas (89%). seqbuster analysis revealed the presence of 70 mirnas […]

PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] have been established for utilizing hts data. the major pipelines include: oasis [], chimira [], mirge [], and tiger [], etc. several tools have also been developed to detect isomirs such as seqbuster [], isomirid [] and deanniso []. one trna detection tool, tdrmapper [], is currently available. for other species of srnas, the majority of the alignment-based pipelines would be sufficient […]

PMCID: 5685733
PMID: 29163812
DOI: 10.18632/oncotarget.21412

[…] each mirna locus. mature mirnas and non-coding rnas were annotated using mirbase (release 21, 2014) and rna central (http://rnacentral.org) respectively. isomir variants were detected using seqbuster [] combined with a panel of in-house perl and r-scripts, which are available upon request. isomirs with mismatches to the genome were discarded from the analysis, as these could […]


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SeqBuster institution(s)
Genetic Causes of Disease Group, Genes and Disease Program, Centre for Genomic Regulation (CRG), Barcelona, Spain; Centro de Investigacion Biomedica en Red en Epidemiologıa y Salud Publica (CIBERESP), Barcelona, Spain; Experimental and Health Sciences Department, Pompeu Fabra University, Barcelona, Catalonia, Spain
SeqBuster funding source(s)
Supported by Spanish Ministry of Health Fondo de Investigaciones Sanitarias (PI081367) and Instituto de Salud Carlos III (CIBERESP), Spanish Ministry of Science and Innovation (SAF2008-00357) the Sixth Framework Programme of the European Commission through the SIROCCO integrated project LSHG-CT-2006-037900, the Spanish Ministry of Science and Innovation (SAF2008-00357), the Spanish Ministry of Health and a fellowship from the Spanish Ministry of Science and Innovation MICINN.

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