Uploading NGS data into EzBioCloud 16S-based MTP app

If you are an EzBioCloud user, you can upload NGS data to the Microbiome Taxonomic Profiling (MTP) pipeline. This is the only way of adding your own data into the EzBioCloud 16S-based MTP app. If you are not ready for being a paid user, please don’t worry. If you are an Academic/Non-profit user, you can upload up to 100 microbiome samples with up to 100,000 NGS reads. [Learn more].

MTP Upload Center

  1. Choose an NGS platform used to generate data.
  2. Choose a taxonomy database. At present, there are three databases to choose from.
    • PKSSU4.0: This is an up-to-date version for the prokaryotic 16S database (Bacteria+Archaea).
    • mtpdb_v1.5: This is a previous version for the prokaryotic 16S database which is provided for the compatibility with old data. If you are new to our service, please choose PKSSU4.0.
    • ATCCSTD1.0: This is a 16S database for analyzing the ATCC® Microbiome Standards.
  3. Choose a target taxon.
  4. The PCR primer sequences in the NGS data may not be accurate as they are the product of annealing. Therefore, we recommend them to be excluded or trimmed. If you want EzBioCloud 16S-based MTP app to trim them, you can select the primer information to be trimmed from the preset or check ‘Custom’ and enter your own primer sequences. Check ‘None’ if you don’t want to trim them or already trimmed the primer sequences.
  5. Upload NGS files here. You can upload the files directly or upload the data via links like ‘Google drive’, ‘Dropbox’, ‘pCloud’. For the paired-end data, both FASTQ files should be uploaded. For PacBio’s ccs data, please upload the processed FASTA data. At present, we will not accept the PacBio’s raw data. If you upload the FASTQ file(s), we will use the quality score data included in the FASTQ format. Files can be compressed by a gzip software (.gz extension) to speed up the uploading process.
  6. Show the status information of your pipeline runs. Please be patient if you are trying the free version since it might take some time. A typical run-time for an MTP for the paid users is less than 30 min.

Make sure that you upload 16S amplicon data generated for Bacteria and Archaea.

Here are some primer sets that are most widely used for microbiome analysis:

  • Illumina paired-end sequencing
    • V3V4 (ChunLab):  341F = CCTACGGGNGGCWGCAG  |  805R = GACTACHVGGGTATCTAATCC
    • V4 (Earth Microbiome Project): 515FB = GTGYCAGCMGCCGCGGTAA  |  806RB = GGACTACNVGGGTWTCTAAT
  • PacBio full-length sequencing
    • 27F = AGRGTTTGATYMTGGCTCAG  |  1492R = GGYTACCTTGTTACGACTT

The EzBioCloud team / Last edited on Sept. 19, 2019