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Analysis Pipelines and Deliverables

Our bioinformatics services include below analysis pipeline, deliverables and data management.

Small genomes and plasmids

Analysis Pipelines

  • Demultiplexing using bcl2fastq
  • QC on raw reads using fastQC which provides quality data on the demultiplexed fastq files

Bacterial genomes are always run through a standard pipeline consisting of:

  • Species and intra species contamination control using kraken2
  • De novo assembly using SPAdes
  • Quality parameters from the de novo assembly using quast

Plasmid sequencing has a standard pipeline consisting of:

  • If de novo assembly using SKESA
  • If reference sequences are provided - mapping with bwa and variant calling with Freebayes.


  • Project delivery report: Containing information about the experimental design
  • Raw data: The fastq files from the demultiplexing
  • de novo assemblies in fasta format
  • bam and vcf files for mapped analysis
  • Quality reports: Individual reports from fastqc, kraken2 and quast

Data management and additional analysis

CTG uses secure LSENS servers hosted by LUNARC, center for scientific and technical computing at Lund University facility, for internal data management and analysis.

Delivery medium

  • All data is by default delivered to the customer via a dedicated secure file server hosted on Lund University.
  • For an additional cost, data can be delivered on a hard disk.
  • For alternative options, please send us an inquiry.

Data storage

The project data will be stored for 3 months.

Additional Services

For additional Bioinformatics services please contact NBIS – National Bioinformatics Infrastructure Sweden, (

Contact for service

CTGservice [at] med [dot] lu [dot] setarget="_self"

CTG Roll-up