Uploading NGS data into BIOiPLUG cloud

If you are a BIOiPLUG 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 BIOiPLUG cloud system. If you are not ready for being a paid user, please don’t worry. You have a free-trial in which you can upload up to 20 microbiome samples with up to 100,000 NGS reads [Learn more].

MTP Upload Center

  1. Choose a taxonomy database. At present, there are three databases to choose from.
    1. PKSSU4.0: This is a up-to-date version for the prokaryotic 16S database (Bacteria+Archaea).
    2. 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.
    3. ATCCSTD1.0: This is a 16S database for analyzing the ATCC® Microbiome Standards.
  2. Choose an NGS platform used to generate data.
  3. Choose a target taxon.
  4. Enter a sample name. It will be used in the subsequent visualizations, so you do not want to use a very long name.  Choose a concise, albeit informative, name. For example, US-AB-7d can be used for the sample from a US citizen who was treated with an antibiotic for 7 days. You can change the sample name later.
  5. Check if you already trimmed the primer sequences or do not want to trim them. 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 BIOiPLUG to trim them, enter the primer information.
  6. Upload NGS files here. 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 gzip software (.gz extension) to speed up the uploading process.
  7. Bring the information about the pipeline ques. Please expect some delays if you are trying the free trial. 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. We expect to launch fungal ITS-based MTP service in 2018.

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 BIOiPLUG team / Last edited on Feb. 25, 2018