How to upload data for Microbiome Taxonomic Profile pipeline

MTP (Microbiome Taxonomic Profile)
08/27/2017
Example files for Microbiome Taxonomic Profile pipeline
10/23/2017

How to upload data for Microbiome Taxonomic Profile pipeline

This document will describe how you can upload NGS data to run Microbiome Taxonomic Profile (MTP) pipeline for the BIOiPLUG cloud platform.

Make sure that you upload 16S amplicon data generated for Bacteria and Archaea. We expect to launch fungal ITS-based MTP service in 2018.

The BIOiPLUG MTP pipeline accepts the following data formats. Files can be compressed by gzip software (.gz extension).

  • Illumina paired-end data as 2 FASTQ files:
    • In this format, two FASTQ files should be uploaded. We recommend providing sequences of both forward and reverse primers, so they are trimmed during the pipeline.
  • Pacific Biosciences ccs (Circular Consensus Sequence) data as single FASTQ/FASTA file:
    • Pacific Biosciences platform can be used to sequence 16S amplicons, typically for the full-length. After Circular Consensus Sequence (ccs) processing, the resultant FASTQ or FASTA format file can be uploaded. The only single file is accepted per a sample. If you sequence with multiple barcodes for a single sample, you need to combine them into a single file.
  • Other NGS platforms as single FASTQ/FASTA file:
    • If sequence quality is reasonably good, you can upload single FASTQ or FASTA file generated by any NGS platform. For Illumina single-end sequencing, please use this.

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
    • 27F = AGRGTTTGATYMTGGCTCAG  |  1492R = GGYTACCTTGTTACGACTT

 

 

Last edited Oct. 23, 2017 (JC)