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Citations per year

Number of citations per year for the bioinformatics software tool riboPicker
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This map represents all the scientific publications referring to riboPicker per scientific context
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Protocols

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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Information


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 citations

 (32)
library_books

Microbiome Dynamics in a Large Artificial Seawater Aquarium

2018
Appl Environ Microbiol
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] e 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 6.8.20 […]

library_books

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

2018
Front Microbiol
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] Popular 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 ). […]

call_split

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

2018
Front Microbiol
PMCID: 5797777
PMID: 29445359
DOI: 10.3389/fmicb.2018.00014
call_split See protocol

[…] dow of 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 v […]

library_books

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

2018
Sci Rep
PMCID: 5792648
PMID: 29386622
DOI: 10.1038/s41598-018-20414-0

[…] e 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 and […]

library_books

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

2018
J Extracell Vesicles
PMCID: 5795766
PMID: 29410780
DOI: 10.1080/20013078.2018.1428004

[…] ls (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 ( […]

library_books

Chloropicophyceae, a new class of picophytoplanktonic prasinophytes

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

[…] sb-roscoff.fr). 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 the de […]


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

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