Parallel-META statistics

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Citations per year

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Popular tool citations

chevron_left Whole genome alignment Microbial taxonomy identification Multiple nucleotide sequence alignment Homology-based taxonomic classification Bioinformatics workflows chevron_right
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Tool usage distribution map

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Associated diseases

Associated diseases

Parallel-META specifications


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


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  • person_outline Kang Ning <>
  • person_outline Xiaoquan Su <>

Publications for Parallel-META

Parallel-META in pipeline

PMCID: 5120256
PMID: 27876778
DOI: 10.1038/srep37376

[…] also removed. this set of high-quality reads was then used for further analysis. the sample taxonomic profile was also determined directly from the metagenome dataset using two online software, i.e. parallel-meta and metaphlan, following the instructions of the two software developers., the microbial illumina reads were assembled into contigs using idba-ud with default parameters. genes […]

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Parallel-META in publications

PMCID: 5541433
PMID: 28768551
DOI: 10.1186/s40168-017-0315-1

[…] 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 […]

PMCID: 5120256
PMID: 27876778
DOI: 10.1038/srep37376

[…] 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 […]

PMCID: 4223665
PMID: 25376098
DOI: 10.1038/srep06957

[…] 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, […]

PMCID: 4165942
PMID: 25227622
DOI: 10.1038/srep06393

[…] the mdv model. the overall scheme is illustrated in :, 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 […]

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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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