Biopieces statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Biopieces

Tool usage distribution map

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

Associated diseases


Popular tool citations

chevron_left Read quality control Read alignment Libraries/frameworks Adapter trimming chevron_right
Want to access the full stats & trends on this tool?


Biopieces specifications


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




No version available


Biopieces citations


Maturation of the gut microbiome and risk of asthma in childhood

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 (, mate-paired and quality filtered (USEARCH v7.0.1090). UPARSE, was used for OTU clustering as recommended, in particular removing singletons after dereplication. Chimera […]


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

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 […]


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

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 ( 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 […]


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

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. […]


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

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 ( 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 […]


Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

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 ( and UPARSE. OTUs were clustered and their abundances were calculated using USEARCH. OTUs were chimera-checked with UCHIME against the Greengenes 2011 database. Singleton […]

Want to access the full list of citations?

Biopieces reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Biopieces