Difference between metadata and manifest file

I am getting confused between manifest and matadata file?

I understand that menifest file contain information about sample ID , path to fastq files and orientation of reads. It generally used to import the fastq files in Qiime2.

In Qiime1, we generally used mapping file so it contaion information about sample id, linkers, barcode, description. It is mention that in Qiime 2 we call this file as matadata file. Where do we exactly use the matadata file? I do not have barcode and linker then should I left these column blank in this file.

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Hi @Yogesh_Gupta,

The manifest helps load your samples in QIIME 2 and name them. This was the sample id, linker, and barcode in your old QIIME 1 mapping file. You use this for demultiplexing your data, but don’t necessarily need it for further analyeses.

The metadata describes your samples: where they come from, when they were collected, how they were treated, etc. You need the same sample ID here as you do in the manifest so you can map your samples to your information. This file is what you need to be able to do statistical analysis and put your samples in context.

Because the two files are separate (demultiplexing and analysis), you don’t need to include the barcode and linker columns in the metadata.


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Thanks a lot.
Can you explain little bit more. My data is already demultiplexed and do not have adapter and barcodes. Then, How should I upload data. In --type SampleData ???should I put multiple pair end reads and how?

I only about ```
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path /project/microbiome_workshop/amplicon/data/manifest.csv
–output-path demux.qza
–source-format PairedEndFastqManifestPhred33


Hi @Yogesh_Gupta,

If this is the case, you should use the manifest format with the command you described. Your manifest will map the sample name to file location on your computer using the absolute path. I usually check the manifest importing directions from the tutorial to make sure I’ve got everything right, but the command looks appropriate as far as I can tell. I think the hardest part can be formatting your manifest, so I often try with a set of test data.


Thank you very much for response and time. now it is clear to me.


Hi @jwdebelius,

I do have one query to you. I have collected these amplicon samples from three different treatment group. When I will add that information to these sample in QIIME2. In qiime1, I have given that information as a description in mapping file.

Hey there @Yogesh_Gupta! Have you had a chance to look at the Metadata guide in the docs?


Also, I suggest you take a look through the Moving Pictures Tutorial to get a high-level overview of how things work in QIIME 2!

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Hi @thermokarst,

I think we do add metadata through this command:

time qiime feature-table summarize \
  --i-table table-dada2.qza \
  --o-visualization table-dada2.qzv \
  --m-sample-metadata-file /project/microbiome_workshop/amplicon/data/mapping.txt
This mapping file should contain same sample ID as we used in manifest file and description about the sample, can I left blank barcode and linker region?

Hi @Yogesh_Gupta!

Yep, you provide metadata to commands (like the one above) via a TSV file.

This question is covered in the Metadata guide I provided above --- those columns are not required.

Hi @thermokarst

Thanks a lot.

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