era7 bioinformatics de novo bacterial genome with pacbio and bg7 pipeline
TRANSCRIPT
August 2016 www.era7bioinformatics.com
Era7 Bioinformatics’ De novo Bacterial Genomics
with PacBio
Bacteria are everywhere
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In the Sea
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In the soil
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In the air
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And in all living organisms
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They can impact positively and negatively Agriculture
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They are crucial in Veterinary
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They can be a serious threat for human health
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Important in biofuel
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And in Biotech and Live Sciences in general
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Knowing bacterial genomes is a key for all Biomedical and Biotech fields. We do that in Era7 Bioinformatics
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The best combination:
•PacBio Sequencing •Era7’s Bioinformatics services
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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)
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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
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De novo Bacterial Genomics with PacBio and BG7 Bioinformatics analysis
We sequenced the same Klebsiella DNA with PacBio and illumina:
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After the HGAP assembly Era7 Bioinformatics’ BG7 pipeline provides a rich and accurate functional annotation
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De novo Bacterial Genomics with PacBio and BG7 Bioinformatics analysis
• 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
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De novo Bacterial Genomics with PacBio and BG7 Bioinformatics analysis
De novo Bacterial Genomics with PacBio and BG7 Bioinformatics analysis
BG7 annotation system pipeline
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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
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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
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Bacterial Genomes with PacBio and BG7
Comparative Genomics Service CG7
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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.
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De novo Bacterial Genomics with PacBio and Era7 Bioinformatics analysis
You can order now!
De novo Bacterial Genomics with PacBio and Era7 Bioinformatics analysis
• http://era7bioinformatics.com
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