MetaAmp protocols

View MetaAmp computational protocol

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MetaAmp specifications

Information


Unique identifier OMICS_18130
Name MetaAmp
Interface Web user interface
Restrictions to use None
Input data A metagenomic sequence.
Input format Fastq, Fasta
Programming languages Javascript, Perl
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline mstrous <>

Publication for MetaAmp

MetaAmp in pipelines

 (2)
2017
PMCID: 5528904
PMID: 28746397
DOI: 10.1371/journal.pone.0181934

[…] reads were merged into single reads using pear 0.9.6 and further processed using metaamp, a 16s rrna data analysis pipeline, developed by the energy bioengineering group (http://ebg.ucalgary.ca/metaamp)[]. raw 16s rrna amplicon sequences are available from the sequence read archive (sra) at ncbi (accession number: samn05467017, http://www.ncbi.nlm.nih.gov/sra/samn05467017). the sequencing […]

2017
PMCID: 5691128
PMID: 29146960
DOI: 10.1038/s41467-017-01544-x

[…] libraries were pooled and normalized for sequencing on the illumina miseq sequencer (san diego, ca) using the 2 × 300 bp miseq reagent kit v3. the resulting amplicon sequences were analyzed with metaamp,. operational taxonomic units (otus) were identified with a threshold of 97% sequence similarity., shotgun metagenomic sequencing (2 × 75 bp) of three replicates of each mock community type […]


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MetaAmp in publications

 (7)
PMCID: 5691128
PMID: 29146960
DOI: 10.1038/s41467-017-01544-x

[…] an average of 5356 high-quality amplicon sequences per replicate (minimum 1686 and maximum 9986 sequences). the amplicon sequences were clustered into 21 operational taxonomic units (otus) using the metaamp pipeline (version 1.3),. four of these otus were identified as illumina in-run cross contaminants from unrelated samples that were sequenced on the same lane. the remaining 17 otus […]

PMCID: 5615460
PMID: 28950879
DOI: 10.1186/s12866-017-1111-6

[…] see additional file . the metaxa2 taxonomic profiles were visualised with a heatmap using ggplot2 in r-studio (see additional file : for settings). metaxa2 extracted ssu reads were run through the metaamp 1.1 pipeline to obtain operational taxonomical unit (otu) abundances., shotgun sequences from each dataset were compared to the ncbi nr database (accessed on 20.01.2016) using diamond […]

PMCID: 5581841
PMID: 28900416
DOI: 10.3389/fmicb.2017.01573

[…] at the department of geosciences, university of calgary. the 300pe reads were merged using pear 0.9.6 with a 50 bp overlap and were further processed with a 420 bp cutoff of amplicon size using metaamp, a 16s rrna data analysis pipeline, developed by the energy bioengineering group, department of geosciences, university of calgary. metaamp was also used for bioinformatic analysis., […]

PMCID: 5528904
PMID: 28746397
DOI: 10.1371/journal.pone.0181934

[…] illumina miseq system at the energy bioengineering group, department of geosciences, university of calgary. the 300pe reads were merged into single reads using pear 0.9.6 and further processed using metaamp, a 16s rrna data analysis pipeline, developed by the energy bioengineering group (http://ebg.ucalgary.ca/metaamp)[]. raw 16s rrna amplicon sequences are available from the sequence read […]

PMCID: 5478722
PMID: 28680423
DOI: 10.3389/fmicb.2017.01164

[…] and quantified using the same procedures as above and sent for illumina miseq sequencing at the university of calgary., analyses of pyrosequencing and illumina miseq sequences were done with the metaamp software, (http://ebg.ucalgary.ca/metaamp/; developed by the university of calgary energy bioengineering group) and sequences were subjected to stringent quality control (qc). merged reads […]


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MetaAmp institution(s)
Department of Geoscience, University of Calgary, Calgary, AB, Canada; Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
MetaAmp funding source(s)
This research was funded by a Campus Alberta Innovation Chair, a NSERC Discovery grant, an Alberta Innovates Technology Futures iCORE grant, a NSERC Banting postdoctoral fellowship, the Government of Canada through Genome Canada, the Government of Alberta through Genome Alberta, Genome Prairie, Research Manitoba and Genome Quebec, and the Canada First Research Excellence Fund.

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