How tos and FAQs

What data will I receive after my sequencing experiment has been finished?

You can receive data (results) in any format you wish. However, if you have no specific requirements, you will receive from us the following standard sequencing outputs:

 


Illumina technology

Data

  • Single-end sequencing – 1 individual FASTQ file for each sub-library (i.e. each index or index combination)
  • Paired-end sequencing – 2 individual FASTQ files (Mate1.fastq and Mate2.fastq) for each sub-library (i.e. each index or index combination)
  • Data will be de-multiplexed based on adaptor index combination and compressed in .gz format.

Reports

  • Sample QC report (passed/not passed, chemistry used and parameters measured)
  • Library QC report (passed/not passed, chemistry used and parameters measured)
  • Sequencing report (basic statistics, chemistry used)
  • Raw data processing description
  • MultiQC report (html format)

 


PacBio technology

Data

  • CLR mode (Continuous Long Read) - CLR reads in BAM and fastq format
  • CCS mode (Circular Consensus Sequencing) – HiFi reads in BAM and fastq format
  • Data will be de-multiplexed according to assigned SMRT adaptor indexes, accompanied with index data file .pbi (e.g. demux.subreads.bam + demux.subreads.bam.pbi and demux.CCS.bam + demux.CCS.bam.pbi)

Reports

  • Sample QC report (passed/not passed, chemistry used and parameters measured)
  • Library QC report (passed/not passed, chemistry used and parameters measured)
  • PacBio SMRT sequencing report (basic statistical data - count of bases and reads, mean read length, N50)

 


Oxford Nanopore technology

Data

  • Data in fast5 format (raw data) as follows:
    • fast5_pass - raw reads before basecalling, which passed quality control
  • Data in FASTQ format as follows:
    • fastq_pass - .fastq passing quality control

Reports

  • Sample QC report (passed/not passed, chemistry used and parameters measured)
  • Library QC report (passed/not passed, chemistry used and parameters measured)
  • Sequencing report (basic statistics, chemistry used)
  • Raw data processing description
  • QC report (html format)

 


Please notice that our bioinformaticians can provide any data output you may need including development of custom data analysis pipelines. For more information please contact us.

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