The 11th Sequencing, Finishing and Analysis in the Future (SFAF) annual meeting will be held June 1-3, 2016 in Santa Fe, NM.
The SFAF meeting - dedicated to bringing together experts in the genomics field - focuses on laboratory methods and computational tools used to help sequence, assemble, and finish genomes.
Our team will introduce our bioinformatics solution for microbial genomics during workshop activities, a tech talk, and a poster presentation.
Workshop
Our pre-SFAF workshop will take place on Tuesday May 31 at 4:00 p.m. - 7:00 p.m in the Santa Fe Room at the La Fonda Hotel.
We offer hands-on training on our Microbial Genomics Pro Suite, which includes CLC Genomics Workbench and a series of plugins that add tools and workflows optimised for microbial genomics and metagenomics. The training includes a free trial and covers
Tech talk
"Analysis of The Functional Contents of Microbial Communities Using a Novel QIAGEN Bioinformatics Pipeline" by Andreas Sand
Poster presentation
"Analysis of Microbial Functions using CLC Microbial Genomics Module" by Marta Matvienko
We're looking forward to seeing you in Santa Fe!
More information about CLC Microbial Genomics Module
More information about SFAF
In the past several months, customers have performed remarkable work with CLC Genomics Workbench, a tool that offers customizable bioinformatics solutions for genomics, transcriptomics, epigenomics, and metagenomics. Many scientists rely on this tool for genome assembly and interpretation every day and here, we look at a handful of recent publications that have been supported by CLC Genomics Workbench.
De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis
First author: Mukesh Jain
This paper in Nature’s Scientific Reports journal comes from scientists in New Delhi who conducted transcriptome sequencing to better understand important biological mechanisms in saffron. They identified transcription factors, differentially expressed genes, and more. The team used CLC Genomics Workbench in the transcriptome assembly and the analysis of differentially expressed genes.
Complete coding sequence of Zika virus from Martinique outbreak in 2015
First author: G. Piorkowski
Scientists in France studied a strain of the Zika virus isolated from a patient in the Caribbean. In this publication, they report the full coding sequence of the virus, an essential resource for the ongoing battle against Zika virus. They used CLC Genomics Workbench to analyze the data generated with an Ion Torrent sequencer.
Effective de novo assembly of fish genome using haploid larvae
First author: Yuki Iwasaki
Published in the journal Gene, this marine genomics study from scientists in Japan demonstrates the utility of sequencing haploid fish larvae — in this case, yellowtail fish — to obtain a diploid genome assembly. They used the Proton sequencer and compared the performance of overlap-layout-consensus (OLC) and de Bruijn graph (DBG) assemblers. CLC Genomics Workbench, which uses a DBG approach, outperformed another tool in the study.
Isolation and Characterization of a Novel Gammaherpesvirus from a Microbat Cell Line
First author: Reed S. Shabman
This study, an editor’s pick in the mSphere journal, comes from scientists at the J. Craig Venter Institute and other organizations who were analyzing the transcriptome of a microbat when they discovered RNA from a previously unidentified herpesvirus. They used CLC Genomics Workbench for assembly and finishing of the viral genome.
Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae
First author: Kai Zhou
In this Scientific Reports paper, scientists from China and the Netherlands tracked the transmission path of a Klebsiella pneumoniae strain using genome-based phylogenetic analysis. They used a mapping unit in CLC Genomics Workbench to find genes associated with antibiotic resistance and pathogen virulence, and detected SNPs by mapping isolate sequence data with the same tool.
Read more about CLC Genomics Workbench
Assembling gold standard reference genomes for microbial pathogens has become fast and easy. We're proud to bring you a new feature allowing rapid error correction and assembly of PacBio data.
The latest version of CLC Genome Finishing Module introduces tools for error-correction and de novo assembly of raw PacBio reads. High quality assemblies can be generated in a fraction of the time that is needed by leading alternatives.
CLC Genome Finishing Module consumes less than 10 percent of the memory used by alternative solutions, while completing the assembly faster. The Module runs on all major operating systems, and fully integrates into the widely used CLC Genomics Workbench and CLC Genomics Server solutions. The included preconfigured workflow makes it extremely user-friendly.
Benchmarking
We compared the performance of the industry standard HGAP1 when run on a high performance computer to the performance of the workflow "PacBio De Novo Assembly Pipeline" included in CLC Genome Finishing Module. Please note that our PacBio De Novo Assembly Pipeline was run on a standard laptop for this comparison.
1Chin et al. (2013), Nature Methods, 10(6), 563–569
Not convinced yet? Try it out
