Experts in phage genome sequencing, assembly, and annotation
Phage characterisation through whole-genome sequencing
By growing phages in host bacterial cells it is possible to obtain enough phage DNA to prepare genomic libraries. At AllGenetics, we use high-throughput sequencing to obtain the annotated genomes of your phages. Phage DNA is purified using specific DNA isolation protocols and the remaining bacterial DNA contamination is deleted bioinformatically after sequencing. Our workflow uses Illumina’s MiSeq technology to obtain the genomes cost-effectively and accurately.
Please note that repetitive genomic regions may be difficult or impossible to assemble using Illumina's short reads. In this case, Illumina's MiSeq sequencing can be complemented with Oxford Nanopore’s MinION or PacBio’s RSII. These are new technologies which provide longer reads that improve genome assembly.
How we work
Step 1: We isolate DNA from your samples using a phage DNA isolation protocol.
Step 2: We prepare genomic libraries using the kits recommended by Illumina.
Step 3: We sequence the libraries using the Illumina MiSeq technology. As a norm, we obtain 5 megabases of raw data per library but we can adapt the output to the genome size of the phage under study.
Step 4: We analyse the high-throughput sequencing data to obtain your annotated genomes.
Please contact us for further information and pricing.
What you receive
A report with a summary of the methods followed.
The raw high-throughput sequencing files.
The results of the bioinformatic analysis including demultiplexing, pre-processing and quality control of the raw data, removal of bacterial reads, de novo assembly, deduplication of clonal reads, automatic gene annotation, and average nucleotide identity between the genomes sequenced.
If you require additional analyses, please let us know and we will do our best to meet your needs.
At no additional cost, our project specialists will be available to you after project delivery and during the editorial process of your scientific articles. We offer up to five 60-min sessions per project, depending on the project size.
What we need
We can start working with either your phage cultures which have been appropriately preserved (fresh or frozen) or your DNA samples which have already been extracted.
If your DNA has already been extracted, we ideally require 20 μL of DNA in TE buffer or water at a minimum concentration of 20 ng/μL and 260/280 and 260/230 absorbance ratios higher than 1.8 per sample.
Please note that, depending on the specifics of your project, these requirements may vary. Please contact us for the specific requirements of your project.