Era7 bioinformatics de novo bacterial genome with pacbio and BG7 pipeline

August 2016 www.era7bioinformatics.com

Era7 Bioinformatics’ De novo Bacterial Genomics

with PacBio

Bacteria are everywhere

www.era7bioinformatics.com

In the Sea


In the soil


In the air


And in all living organisms


They can impact positively and negatively Agriculture


They are crucial in Veterinary


They can be a serious threat for human health


Important in biofuel


And in Biotech and Live Sciences in general


Knowing bacterial genomes is a key for all Biomedical and Biotech fields. We do that in Era7 Bioinformatics


The best combination:

•PacBio Sequencing •Era7’s Bioinformatics services


De novo Bacterial Genomics with PacBio and BG7 Bioinformatics analysis

The length of the reads of PacBio allows solving the main problems of the short reads: • the assembly of regions repeated along the genome

(sequences with several copies) • the non-homogeneous coverage of the genome

(regions with low coverage)


Thanks to the random distribution of base-calling errors, PacBio allows the correction of the final assembly.

It is important to consider that when the errors are always located in the same regions a higher coverage never gets to improve the error rate



We sequenced the same Klebsiella DNA with PacBio and illumina:


https://era7bioinformatics.com/en/page.cfm?id=965&title=era7-last-research-posters

After the HGAP assembly Era7 Bioinformatics’ BG7 pipeline provides a rich and accurate functional annotation



• BG7 is a system for genome annotation of bacteria sequenced with Next-gen sequencing technologies

• BG7 does exhaustive gene prediction integrated with rich functional annotation.

• It is especially good for new genomes without taxonomically close known genomes in databases




BG7 annotation system pipeline


http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049239

Features of BG7 annotation system:

• ORF prediction based on the detection of similarity with Uniprot proteins

• Annotation customised to client specific goals: metabolic pathways, antibiotic resistance, vaccine development, virulence genes, secondary metabolite biosynthesis, ...

• Tolerant to NGS-specific errors • It detects genes even if they are fragmented or have insertions,

deletions or substitutions in their sequences


Bacterial Genomes with PacBio and BG7

Our results with BG7: • A quick and complete annotated genome, close to

manually annotated genomes • A genome rich in functional annotations (GO,

Interpro, EC, references) • Deliverables compliant with freely available tools

and browsers: Artemis, Mauve, EBI tools, IGV


Bacterial Genomes with PacBio and BG7

Comparative Genomics Service CG7


Comparative genomics for PacBio genomes We have a very complete comparative genomics pipeline. You can select the complete pipeline or select only the modules most interesting for your research.

In the set of genomes for comparative analysis you can include your new PacBio genomes and any other complete genome. The practically closed genomes that Pacbio provides, make the comparisons much more reliable. In addition, it is possible to detect changes in genes with several copies (RNA operon, transposases) or in repetitive regions.




De novo Bacterial Genomics with PacBio and Era7 Bioinformatics analysis

You can order now!

De novo Bacterial Genomics with PacBio and Era7 Bioinformatics analysis

• [email protected]

• http://era7bioinformatics.com


https://era7bioinformatics.com/en/page.cfm?id=510&title=bacterial-genomes-with-pacbio

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