Biopieces protocols

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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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Documentation


Biopieces in pipelines

 (4)
2017
PMCID: 5746284
PMID: 29240831
DOI: 10.1371/journal.ppat.1006767

[…] on an illumina hiseq 1500., quality assessment of 100 nucleotide paired-end reads was performed via an initial evaluation with fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and biopieces (http://biopieces.org). illumina sequencing adapters and low quality sequences were removed with trimmomatic []. the remaining sequences were mapped separately against the esmeraldo […]

2016
PMCID: 4789741
PMID: 26972923
DOI: 10.1038/srep22954

[…] reads for dna and rna viromes from blighted mats, respectively, and 329,685 and 31,032 for dna and rna viromes from normal cyanobacterial mats, respectively ()., primer sequences were removed using biopieces (hansen, m. a. www.biopieces.org; unpublished), and the prinseq suite of tools was used for quality filtering as previously described. raw sequences and contigs were assembled using newbler […]

2015
PMCID: 4832382
PMID: 26278404
DOI: 10.1111/mmi.13169

[…] located at the university of maryland, college park. the quality of read datasets (sanger fastq format) was determined using fastqc (ramirez‐gonzalez et al., ); data were filtered and trimmed using biopieces (biopieces.org) to select for reads containing the tn‐seq barcodes and krmit itr ends. reads were then de‐multiplexed and count tables generated using samtools (li et al., ) and htseq […]

2014
PMCID: 3913684
PMID: 24503942
DOI: 10.1371/journal.pone.0087924

[…] parameters: --pre_correction --num_threads 16 --min_contig 200. adapter sequences in the 454 reads were detected and removed by prinseq-lite 0.19.2 . 454 reads with low quality were removed using biopieces with the following parameters: mean quality threshold of 20, local quality threshold of 15 with a 5 nt sliding window. de novo assembly of 454 reads was performed using newbler 2.6 (roche). […]


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Biopieces in publications

 (30)
PMCID: 5762761
PMID: 29321519
DOI: 10.1038/s41467-017-02573-2

[…] samples were sequenced per run., 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 […]

PMCID: 5622210
PMID: 28993764
DOI: 10.3389/fmicb.2017.01832

[…] 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 […]

PMCID: 5501559
PMID: 28683715
DOI: 10.1186/s12870-017-1070-y

[…] by nanodrop spectrophotometry (concentration, a260/a280 of approximately 1.8 or more) and gel electrophoresis (high molecular weight, integrity, purity)., 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 […]

PMCID: 5569705
PMID: 28575281
DOI: 10.1093/nar/gkx483

[…] 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., a previously published algorithm was used to identify putative target sites for artificial […]

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

[…] to nematode-specific bands were sequenced (macrogen, amsterdam, the netherlands)., 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 […]


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