riboPicker 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 IN pipelines

 (2)
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 […]

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

[…] site and 2,626,578 and 2,228,065 sequences for the downstream site. quality filtering via fqtrim removed 19% and 37% of the upstream sequences and 26% and 32% of the downstream sequences, whereas ribopicker removed 942 sequences from the upstream sample and 285 sequences for the downstream sample. bowtie 2 revealed 0.02% human contamination in both sample site metagenomes, with 174 sequences […]

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

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