riboPicker protocols

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riboPicker specifications

Information


Unique identifier OMICS_02618
Name riboPicker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Unique identifier OMICS_02618
Name riboPicker
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Publication for riboPicker

riboPicker in pipelines

 (8)
2017
PMCID: 5382025
PMID: 28409117
DOI: 10.1016/j.gdata.2017.03.010

[…] fastq filter quality (http://hannonlab.cshl.edu/fastx_toolkit). since rna sequencing data contained rrna sequences it was necessary to conduct the removal of rrna sequences from the raw data using ribopicker tool. the resulting data set was assembled with trinity (version 20130814) in accordance with the guidance provided by the developers, and the default settings. to identify retroelements […]

2017
PMCID: 5656628
PMID: 29070840
DOI: 10.1038/s41598-017-12412-5

[…] the quality of the reads was checked by fastqc v.0.52 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). reads were separated into ribosomal and non-ribosomal sequences with ribopicker v.0.4.3 using as a reference the small subunit rna database (ssr database) from the silva project (release 119). ribosomal and non-ribosomal sequences were assembled separately using […]

2017
PMCID: 5787841
PMID: 28703416
DOI: 10.1111/pbi.12793

[…] 2000 platform (100 bases paired‐end reads; illumina, san diego, ca). quality control and rrna content were assessed, and nondesired reads masked for further analyses with fastqc (andrews, ) and ribopicker (rrnadb_2012‐01‐17 release; schmieder et al. ()). no comprehensive reference transcriptome was available for brassica oleracea. recently published b. oleracea genome v1.0 (liu et al., ) […]

2016
PMCID: 4772301
PMID: 26926518
DOI: 10.1186/s12864-016-2501-0

[…] of 0.01, to the 3’ end) and sequencing adapters were trimmed using custom java scripts., the preprocessed metatranscriptome reads were further processed to remove any rrna fragments, using ribopicker v0.4.3 [] with thresholds of 90 % alignment coverage and 90 % alignment identity. blastx [] was then used to align the reads against the nr database to obtain the best-hit sequence […]

2016
PMCID: 5221468
PMID: 27506856
DOI: 10.1002/mbo3.392

[…] dna in fastq format were quality filtered, trimmed and adapters, unknown terminal bases, poly‐a tails, and low‐quality 3′ read regions were removed via fqtrim (pertea, ). paired‐ends were joined and ribopicker was used to remove 16s, 18s, 28s, and 5.8s ribosomal rna to increase the quality of sequences and relevance of the results (schmieder, lim, & edwards, ). bowtie 2 was used to remove […]


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riboPicker in publications

 (28)
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] metagenome, reads were merged by using flash v. 1.2.9 (), and the resulting fastq files were submitted to the ncbi sequence read archive. ribosomal reads were removed from the merged reads by using ribopicker (). non-rrna reads were queried against the ncbi nr database with diamond (), using blastx and a minimum bit score of 50. the output was imported into megan community edition version […]

PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] filter tools are read mappers such as bowtie (langmead, ; langmead and salzberg, ) and bwa (li and durbin, ), while specialized software, such as human best match tagger (bmtagger, ncbi, ) or ribopicker (schmieder, ), is less commonly used (table )., workflows are sorted by: availability of a graphical user-interface (yes-no), runtime (fast-slow), and availability (yes-limited-no). ?: […]

PMCID: 5797777
PMID: 29445359
DOI: 10.3389/fmicb.2018.00014

[…] 3 and step of 1 with a minimum mean quality score of 20, trim >5 uncalled bases from ends, trim >5 a/t tails, and allow only 1 uncalled base (any reads with uncalled bases were later removed). ribopicker (version 0.4.3; schmieder et al., ) was used to identify rrna reads in metatranscriptome libraries. the default parameters (50% coverage, 75% identity, 30 base align length, bwa-sw z-best […]

PMCID: 5792648
PMID: 29386622
DOI: 10.1038/s41598-018-20414-0

[…] quality-filtered (leading:20, trailing:20, slidingwindow:4:20, minlen:100) and adaptors were removed using trimmomatic software (v0.33). shotgun reads matching the 16s rrna gene were selected using ribopicker (standalone-0.4.3) after reads alignment on silva and ribosomal database project (rdp) databases. paired-end reads were merged using flash (v1.2.11) using options (−m 80) for amplicons […]

PMCID: 5795766
PMID: 29410780
DOI: 10.1080/20013078.2018.1428004

[…] (wormbase ws255; http://parasite.wormbase.org; []) using the star transcriptome aligner []. prior to downstream analysis, rrna-like sequences were removed from the metatranscriptomic dataset using ribopicker-0.4.3 (http://ribopicker.sourceforge.net; []). blastn algorithm [] was used to compare the non-redundant mrna dataset for t. muris evs to the nucleotide sequence collection (nt) from ncbi […]


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riboPicker institution(s)
Department of Computer Science, San Diego State University, San Diego, CA, USA

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