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CBiB - Bordeaux Bioinformatics Center
The Center for Bioinformatics (CBiB) provides access to high-performance computing resources, data analysis and programming expertise
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Developments in next generation sequencing – June 2014 edition

Developments in next generation sequencing – June 2014 edition | CBiB - Bordeaux Bioinformatics Center | Scoop.it
This is the third edition of this visualisation, previous editions were in October 2013 and December 2012. As before, full run throughput in gigabases (billion bases) is plotted against single-end ...
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2014 khmer protocols

Making de novo assembly cheap & easy: standardized protocols for mRNAseq and metagenome assembly and analysis C. Titus Brown Assistant Professor CSE, MMG, B
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Genome Biology | Abstract | TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Genome Biology | Abstract | TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes | CBiB - Bordeaux Bioinformatics Center | Scoop.it
Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise.
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BMC Bioinformatics | Abstract | Finishing bacterial genome assemblies with Mix

BMC Bioinformatics | Abstract | Finishing bacterial genome assemblies with Mix | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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Dmitry Alexeev's curator insight, October 20, 2013 4:32 AM

one more to the genomic moneybox of assembley algorithms

 

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Illumina Announces Moleculo Long Read Technology and Phasing As Service

Illumina Announces Moleculo Long Read Technology and Phasing As Service | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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RF: A method for filtering short reads with tandem repeats for genome mapping.

RF: A method for filtering short reads with tandem  repeats for genome mapping. | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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Nucleotide BLAST: Search nucleotide databases using a nucleotide query

Nucleotide BLAST: Search nucleotide databases using a nucleotide query | CBiB - Bordeaux Bioinformatics Center | Scoop.it
CBiB's insight:

Improved microbial BLAST has new database options including Representative genomes plus links to Entrez Genome

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Applications for PacBio circular consensus sequencing

Applications for PacBio circular consensus sequencing | CBiB - Bordeaux Bioinformatics Center | Scoop.it
I am a fan of the Pacific Biosciences PacBio RS sequencing instrument, as some of the readers of this blog maybe already are aware of. We use data from this instrument in our work, and the Norwegia...
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The CBiB Quality Management System is approved - ISO 9001:2008

The CBiB Quality Management System is approved - ISO 9001:2008 | CBiB - Bordeaux Bioinformatics Center | Scoop.it
CBiB's insight:

The CBiB - Bordeaux Bioinformatics Center has been approved by Lloyd's Register Quality Assurance to the following Quality Management System Standards : ISO 9001:2008

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Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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PLOS Computational Biology: Ten Simple Rules for the Open Development of Scientific Software

PLOS Computational Biology: Ten Simple Rules for the Open Development of Scientific Software | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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PLOS ONE: Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

PLOS ONE: Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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How to sequence a bacterial genome at the end of 2012

How to sequence a bacterial genome at the end of 2012 | CBiB - Bordeaux Bioinformatics Center | Scoop.it
A potential user (‘customer’) of our sequencing platform asked how to generate reference genomes for his 4 bacterial strains. His question inspired me to write this post. The suggestion...
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Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements

Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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Arjen ten Have's curator insight, January 29, 10:01 AM

It seems hierarchic strategies for sequencing are back!

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BMC Bioinformatics | Abstract | Sequencing error correction without a reference genome

BMC Bioinformatics | Abstract | Sequencing error correction without a reference genome | CBiB - Bordeaux Bioinformatics Center | Scoop.it
Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output.
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Tutorials

Tutorials | CBiB - Bordeaux Bioinformatics Center | Scoop.it
CBiB's insight:

Everything You Always Wanted to Know About Genome Assembly* (*But Were Afraid to Ask)

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End of Short-Read Era? - (Part I) - Homologus

End of Short-Read Era? - (Part I) - Homologus | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools | BMC Genomics

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools | BMC Genomics | CBiB - Bordeaux Bioinformatics Center | Scoop.it
De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity.
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Dmitry Alexeev's curator insight, April 22, 2013 1:04 PM

a lot ... A LOT ... on genomic tools comparisons

 

Dmitry Alexeev's curator insight, July 28, 2013 7:21 AM

fine review and test for available techniques

 

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Drilling into big cancer-genome data : Nature Methods : Nature Publishing Group

Drilling into big cancer-genome data : Nature Methods : Nature Publishing Group | CBiB - Bordeaux Bioinformatics Center | Scoop.it
Paving roads through data mountains, consortia are developing workflows and tools for widespread use.
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Genome reassembly with high-throughput sequenci... [BMC Genomics. 2013] - PubMed - NCBI

Genome reassembly with high-throughput sequenci... [BMC Genomics. 2013] - PubMed - NCBI | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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Genome Biology | Abstract | CGAL: computing genome assembly likelihoods

Genome Biology | Abstract | CGAL: computing genome assembly likelihoods | CBiB - Bordeaux Bioinformatics Center | Scoop.it
Assembly algorithms have been extensively benchmarked using simulated data so that results can be compared
CBiB's insight:

Find N50 too simplistic as an assembly quality metric? The Pachter lab present a more sophisticated approach.

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Dmitry Alexeev's curator insight, February 4, 2013 2:05 AM

this is biota case - where you never have a general truth genome

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Ten things to consider when choosing an NGS supplier

Ten things to consider when choosing an NGS supplier | CBiB - Bordeaux Bioinformatics Center | Scoop.it
Top ten lists have taken a bit of a battering in recent times, and so I kind of apologise for adding another one, but I’m not really that sorry. Some of you will be aware that I manage a geno...
CBiB's insight:

Pay attention particularly on point 4: #Bioinformatics ;) 

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Best wishes for 2013 from the CBiB's team

Best wishes for 2013 from the CBiB's team | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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Developments in next generation sequencing – a visualisation

Developments in next generation sequencing – a visualisation | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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PLOS Computational Biology: Bioinformatics for the Human Microbiome Project

PLOS Computational Biology: Bioinformatics for the Human Microbiome Project | CBiB - Bordeaux Bioinformatics Center | Scoop.it
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