Biopieces statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Biopieces
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Tool usage distribution map

This map represents all the scientific publications referring to Biopieces per scientific context
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Associated diseases

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Popular tool citations

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Protocols

Biopieces specifications

Information


Unique identifier OMICS_01036
Name Biopieces
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl, Python, Ruby, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Biopieces citations

 (21)
call_split

Maturation of the gut microbiome and risk of asthma in childhood

2018
Nat Commun
PMCID: 5762761
PMID: 29321519
DOI: 10.1038/s41467-017-02573-2
call_split See protocol

[…] Fastq-files demultiplexed by the MiSeq Controller Software (Illumina Inc.) were trimmed for amplification primers, diversity spacers, and sequencing adapters using biopieces (www.biopieces.org), mate-paired and quality filtered (USEARCH v7.0.1090). UPARSE, was used for OTU clustering as recommended, in particular removing singletons after dereplication. Chimera […]

library_books

Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation

2017
Front Microbiol
PMCID: 5622210
PMID: 28993764
DOI: 10.3389/fmicb.2017.01832

[…] eq reagent kit v2 (500cycles) and a MiSeq sequencer (Illumina Inc., San Diego, CA, United States).Sequence analyses were prepared as follows: paired-end reads were mated and trimmed for primers using Biopieces. Reads were quality-filtered with UPARSE () with the following parameters: max expected error algorithm with –maxee 0.5. Dereplication was performed and singletons removed. OTUs were cluster […]

call_split

Plant RRBS, a bisulfite and next generation sequencing based methylome profiling method enriching for coverage of cytosine positions

2017
BMC Plant Biol
PMCID: 5501559
PMID: 28683715
DOI: 10.1186/s12870-017-1070-y
call_split See protocol

[…] In silico digestion was performed using biopieces v0.48 (www.biopieces.org) of the A. thaliana (TAIR 10), B. vulgaris ssp. vulgaris, B. rapa, O. sativa ssp. indica version 9311_BGF_2005, O. sativa ssp. japonica, and Z. mays (B73) nuclear re […]

library_books

Knockdown and replacement therapy mediated by artificial mirtrons in spinocerebellar ataxia 7

2017
Nucleic Acids Res
PMCID: 5569705
PMID: 28575281
DOI: 10.1093/nar/gkx483

[…] Libraries were sequenced on a Genome Analyzer IIx for 36 cycles following the manufacturer's protocols. Illumina's GA Pipeline was used for image analysis and base calling. Adaptors were trimmed with Biopieces remove_adapter script, and remaining sequences were aligned against full-length mirtron hairpins. […]

library_books

Microbiomes associated with infective stages of root knot and lesion nematodes in soil

2017
PLoS One
PMCID: 5417685
PMID: 28472099
DOI: 10.1371/journal.pone.0177145

[…] Sequence demultiplexing was done using the MiSeq Controller Software and diversity spacers were trimmed using Biopieces (www.biopieces.org). Sequence mate-pairing and filtering was done using Usearch v7.0.1090 [].For bacterial 16S rRNA gene sequences, OTU clustering, dereplication and singleton removal was pe […]

call_split

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

2017
Sci Rep
PMCID: 5382530
PMID: 28383027
DOI: 10.1038/srep45691
call_split See protocol

[…] sequencer (Illumina Inc., San Diego, CA, U.S.A). Additional information regarding sequencing conditions and processing methods is provided in . Briefly, paired end reads were merged and trimmed using Biopieces (www.biopieces.org) and UPARSE. OTUs were clustered and their abundances were calculated using USEARCH. OTUs were chimera-checked with UCHIME against the Greengenes 2011 database. Singleton […]


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