MetaAmp Version 2.0

The MetaAmp is designed for analyzing universally conserved phylogenetic marker genes (e.g. 16S/18S rRNA) of metagenomic data. It clusters amplicon reads into OTUs and generates diversity indices and taxonomic composition of the input communities . It accepts single-read or paired-end sequencing in fasta or fastq format from various sequencing platforms (e.g. 454, MiSeq). For additional information on how to run MetaAmp, click

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For what kind of analysis results MetaAmp can produce, click Mock community analysis results

Please cite the following: Dong X, Kleiner M, Sharp CE, Thorson E, Li C, Liu D and Strous M (2017) Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp. Front. Microbiol. 8:1461. doi: 10.3389/fmicb.2017.01461

Analysis Name:
Email address:
Sequence format:
Fastq   Fasta
Sequencing type:
Paired-end   Single
Upload archived sequence file (demultiplexed):
Upload mapping file (text format):
Forward amplicon primers (5'->3'):
Reverse amplicon primers (5'->3'):
Marker gene type:
rRNA Gene   non-rRNA Gene
Similarity cutoff:


Paired end merging options

Minimum length of overlap:
Maximum number of mismatches in the overlap region:

Quality filtering options

Maximum number of differences to the primer sequence:
Maximum number of expected errors:
Trim amplicon to a fixed length:
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