Life Science/Next Generation Sequencing/

Metagenome Analysis

Shotgun metagenomic sequencing

 

Identifies Bacteria, Archaea, Virus, Fungi and Eukaryotes in one shot

 

• Quantification of gDNA
• DNA sequencing library preparation using Illumina Nextera Flex/NEBNext® Ultra™ II FS DNA Library Prep
• Only 50 ng of gDNA required
• Sequencing preparation tagged with barcoded adapters for multiplexing
• Size selection to a major fragment size of 200-800 bp
• Library check
• Sequencing / 150 nt / PE / 50 mio reads / 7.5 Gb
• Paired-end sequencing, read length 150 nt, NextSeq 500™
• Sequencing preparation
• Qubit/dilution
• Data storage and conversion
• Index managemt and de-multiplexing
• Data delivery via download

 

Price for 1-4 samples : 570,- €/sample
Price for 5-9 samples: 550,- €/sample
Price from 10 samples: 530,- €/sample

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Bioinformatic analysis of shotgun metagenomic data:

Kraken2* Metagenomic Analysis

 

The Kraken Metagenomics workflow assigns taxonomic labels to short DNA sequences with high sensitivity and speed using exact alignments of k-mers and a novel classification algorithm.

Outputs:

 

– Krona charts for interactive exploration of each sample
– classified samples
– tab-delimited kraken-report in different formats including:

  1. percentage of reads covered by the clade rooted at this taxon
  2. Number of reads covered by the clade rooted at this taxon
  3. Number of reads assigned directly to this taxon
  4. A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies.
  5. NCBI taxonomy ID
  6. Indented scientific name
    • Shannon diversity, a measure of the biodiversity observed in the sample
    • The number of species observed in the sample

The database being used includes the following reference libraries:

  • archaea: RefSeq complete archaeal genomes/proteins
  • bacteria: RefSeq complete bacterial genomes/proteins
  • viral: RefSeq complete viral genomes/proteins
  • human: GRCh38 human genome/proteins
  • fungi: RefSeq complete fungal genomes/proteins
  • plant: RefSeq complete plant genomes/proteins
  • protozoa: RefSeq complete protozoan genomes/proteins

*Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46. http://genomebiology.com/2014/15/3/R46

Microbial DNA preparation service from various starting material:

 

StarSEQ has long term and advanced knowledge in extracting DNA from a wide range of starting material. We adjust varied DNA extraction protocols, kits and bead mill grinding to meet the individual demands of any project. We are using the most advanced tissue homogenizer from Bertin (Precellys Evolution and Minilys) for optimal adapted sample preparation.

Our experience covers almost all kind of genetic material:

 

• All kind of tissues and blood

• Swabs from skin and other surfaces

• Fecal samples

• Saliva samples

• Soil and sludge

• Sediments

• Water and liquids

• Air filter

• Biofilms

• Nutriments

 

Starting from 18€/sample

Bacterial-seq promotion!

 

Sequencing of bacterial genomes to 100 fold coverage

 

• Quantification of gDNA
• DNA sequencing library preparation
• Enzymatic fragmentation
• Only 10-100 ng of gDNA required
• Sequencing preparation tagged with barcoded adapters for multiplexing
• Library check
• Sequencing preparation

• Paired-end sequencing, read length 150 nt, NextSeq 500™
• Qubit/dilution
• Data storage and conversion
• Index managemt and de-multiplexing
• Data delivery via download

 

Optional: Bioinformatic services

  1. De novo assembly to contigs using SPAdes Genome Assembler: 30 €/sample (1-3 Mb), 40 €/sample (5-15 Mb)
  2. Bacterial analysis: identifying antimicrobial resistance genes + MLST analysis + search for plasmid replicons + plasmid MLST analysis: 50 €/sample
  3. Prokka Genome Annotation – annotation of genes and identifying coding sequences in prokaryotic genomes: 30 €/sample (Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014 Jul 15;30(14):2068-9. PMID:24642063)

1 Mb genome size, 650 k reads: 195 €

 

2 Mb genome size, 1.5 M reads: 205 €

 

3 Mb genome size, 2 M reads: 215 €

 

5 Mb genome size, 3.3 M reads: 235 €

 

8 Mb genome size, 5.3 M reads: 265 €

 

10 Mb genome size, 6.6 M reads 280 €

 

15 Mb genome size, 10 M reads 320 €

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