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Protocols

Parallel-META specifications

Information


Unique identifier OMICS_01519
Name Parallel-META
Alternative name Parallel-META 3
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Kang Ning
  • person_outline Xiaoquan Su

Publications for Parallel-META

Parallel-META citations

 (7)
call_split

Feed additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken

2017
Microbiome
PMCID: 5541433
PMID: 28768551
DOI: 10.1186/s40168-017-0315-1
call_split See protocol

[…] olymer runs in excess of 8 bases, were removed using Parallel-QC [] and QIIME []. Then the sequences were checked for chimeras using UCHIME [] and assigned to operational taxonomic units (OTUs) using Parallel-META [, ] with a 97% threshold of pairwise identity, and then classified taxonomically using the Green genes reference database []. To standardize sequence counts across samples with uneven s […]

library_books

Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits

2016
Sci Rep
PMCID: 5120256
PMID: 27876778
DOI: 10.1038/srep37376

[…] a using a more traditional approach based on 16S rRNA amplicon sequencing, we also extracted the taxonomic profiles directly from the metagenome dataset by using two publicly accessible online tools, Parallel-META and MetaPhlAn (). We found some discrepancies between the phylogenic metagenome profiles as determined by the three methods; such discrepancies are possibly caused by the differences in […]

call_split

Fungal Community Associated with Dactylopius (Hemiptera: Coccoidea: Dactylopiidae) and Its Role in Uric Acid Metabolism

2016
Front Microbiol
PMCID: 4917543
PMID: 27446001
DOI: 10.3389/fmicb.2016.00954
call_split See protocol

[…] Ribosomal genes from all metagenomic reads were obtained using Parallel-meta 2.4 (Su et al., ) algorithm. Eukaryotic ribosomal sequences were recovered using -E option against the SILVA database within an e-value of 1 × 10−10 cutoff. Fungal 18S rRNA sequences wer […]

library_books

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

2015
Front Genet
PMCID: 4681832
PMID: 26734060
DOI: 10.3389/fgene.2015.00348

[…] ore conditions following a statistical procedure with some normalization step (Rodriguez-Brito et al., ; Pookhao et al., ). Some useful tools to perform robust comparative functional metagenomics are Parallel-meta and MEGAN. Other more specialized software are capable of returning graphical representations of metabolic abundances and taxonomic correlations as heatmaps or PCA plots of communities c […]

library_books

Assessment of quality control approaches for metagenomic data analysis

2014
Sci Rep
PMCID: 4223665
PMID: 25376098
DOI: 10.1038/srep06957

[…] n Dataset E, rate of targeting reads was raised up to 96.3% on average by QC-Chain in the post-QC data (). We further evaluated the effect of the QC process by downstream comparison analysis. We used Parallel-META to generate the microbial community structures, and then calculated the similarity of structures based on Meta-Storms with mixed data and post-QC data to the targeting data, respectively […]

library_books

Rapid comparison and correlation analysis among massive number of microbial community samples based on MDV data model

2014
Sci Rep
PMCID: 4165942
PMID: 25227622
DOI: 10.1038/srep06393

[…] The community structure profiles of all samples are parsed out from their 16S rRNA gene sequences by high efficient metagenomic analysis tool Parallel-META (version 2.0). Parallel-META maps the 16S rRNA sequences of each sample by MegaBLAST to the reference database to identify the taxonomical classification and phylogenetic relationship of […]

Citations

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Parallel-META institution(s)
Single-Cell Center, Shandong Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao, China; Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
Parallel-META funding source(s)
Supported by grants from National Natural Science Foundation of China [61303161], Ministry of Science and Technology [2014AA21502], Open Fund of Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences [KLMEES201304], and Soil Microbiome Program, Chinese Academy of Sciences [XDB15040100].

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