Strand NGS v2.7 released

We are excited to share the release of Strand NGS v2.7. This new version comes with several exciting features and enhancements. Listed below are few major enhancements:

  • Strand NGS v2.7 is upgraded to work with Java 1.8 and supports Mac EI Capitan OS
  • New SNP caller feature ‘Low frequency SNP detection’ introduced
  • Split alignment feature enhanced to support circular genome
  • Additional pre-processing step ‘Split read realignment’ added to DNA-Seq workflow
  • Speed of SNP annotation time for targeted re-seq experiments reduced by up to 95% with use of dbSNP sub-setting script. This new option enables user to create and save subset of dbSNP database with target regions of interest.
  • ‘Find Damaging NS Variants’ feature improved to includes:
    i.   Predictions from MutationAssessor, FATHMM, MetaSVM, MetaLR
    ii.  Allele frequency information from ExAC, ESP in addition to 1000 genomes
    iii. Filtering options using conservation scores from phyloP and phastcons
  • Improvements made to features like Local realignment, filtering, variant calling, jobs monitor, import/export options and many more.

To know more, please read the release notes. To enjoy these great features click on Update product from Help Menu.

Review of selected publications citing Strand NGS

In 2015, we brought in many new features and improvements based on your requirements and feedback. We expanded the Strand NGS epigenomics toolkit by adding the MeDIP-Seq workflow in the v2.5 release. We also added new features like the alignment workflow and SV detection for split reads (watch the webinar), a browser-based copy number variation (CNV) view (watch the webinar), and correlation analysis. 2015 was also a year with some great publications that cited Avadis NGS and Strand NGS. Here is a small selection:

K-bZIP Mediated SUMO-2/3 Specific Modification on the KSHV Genome Negatively Regulates Lytic Gene Expression and Viral Reactivation (Wan-Shan Yang, et al.) published in PLoS Pathogens. The authors looked at ChIP-Seq data as well as RNA-Seq data to study the association of SUMO paralog genome modifications with KSHV (one of the seven known human oncoviruses) reactivation. Avadis NGS was used to align ChIP-Seq data to the KSHV genome build and to delineate the SUMO-1 and SUMO-2/3 binding patterns. RNA-Seq reads that did not align with hg19 were mapped with the KSHV genome in Avadis NGS and differential gene expression was determined based on sample wise transcript RPKM values reported by Avadis NGS and verified by RT-qPCR.

Novel roles for LIX1L in promoting cancer cell proliferation through ROS1-mediated LIX1L phosphorylation (Satoki Nakamura, et al.) published in Nature Scientific Reports. The authors report novel roles of Limb expression 1-like (LIX1L) in promoting cancer cell proliferation through ROS1- mediated LIX1L phosphorylation in oesophagus, gastric, breast, lung, thyroid, ovarian, kidney, liver, colon, prostate and pancreatic cancers. Strand NGS was used for alignment, filtering, quantification and statistical analysis of small RNA sequencing data, as well as prediction of miRNA targets.

Lysine-specific demethylase LSD2 suppresses lipid influx and metabolism in hepatic cells (Katsuya Nagaoka, et al.) published in Molecular and Cell Biology. The authors integrated transcriptomic, metabolomic and ChIP-Seq data to demonstrate the role of LSD2 in homeostatic control of the lipid metabolism in mouse hepatocytes. Avadis NGS was used to analyze and visualize the ChIP-Seq data.

Sex Specification and Heterogeneity of Primordial Germ Cells in Mice (Akihiko Sakashita,et al.) published in PLoS One. The authors report on female and male specific gene expression in the mouse primordial germ cells and the complex gene expression networks involved in PGC sex differentiation. RNA-Seq data analysis including quantification, normalization, fold change analysis and principal component analysis (bi-dimensional PCA) was performed in Strand NGS.

Congratulations to these authors and all the others who have seen their research efforts rewarded with a publication of their work.

Webinar on Strand NGS Pipeline Manager for streamlining large scale analysis

This webinar, will highlight the Strand NGS Pipeline Manager feature. In this webinar, you will learn how to customize pipelines and share them with other Strand NGS users. This webinar will give a brief glimpse of an elaborate pipeline that aligns reads, filters poor-quality matches, computes coverage metrics, identifies variants, checks for sample cross-contamination, and emails quality reports – all from within Strand NGS. Vamsi will also be available for live questions at the event.

Speaker: Dr. Vamsi Veeramachaneni, Vice President – Bioinformatics, Strand Life Sciences

Details:
Session 1: 02:30 PM IST; 24 Feb 2016
Session 2: 10:30 PM IST; 24 Feb 2016

Register at http://www.strand-ngs.com/webinar_registration

Meet us at ASHG 2015!

We are excited to be a part of the Annual Meeting of The American Society of Human Genetics (ASHG) again, this time in Baltimore, Maryland from 6- 10 October 2015. Come and meet us to learn more about our best-in-class next-generation sequencing (NGS) data analysis software Strand NGS and Agilent Technologies state-of-the-art multi-omics analysis software GeneSpring.

You can meet our representatives for a one-on-one discussion or a live demo of Strand NGS and GeneSpring suite at Agilent Technologies booth #701. To schedule a demo / one-on-one meeting, please write to us at sales@strandngs.com

The Strand team will also present four posters at the ASHG conference this year. One of our posters titled ‘Detection of translocations in clinical cancer samples using targeted NGS data‘, presented as part of the ‘Clinical Genetic Testing’ has scored high points by the ASHG reviewers committee and will feature among the top 10%, so make sure you mark your calendars to come and take a look. The other three posters will be presented in the ‘Bioinformatics and Genomic Technology’ sessions. Listed below are the details

 

Date: 7th Oct 2015

Session: Bioinformatics and Genomic Technology

Date: 8th Oct 2015

Session: Clinical Genetic Testing

Session: Bioinformatics and Genomic Technology

Webinar on Detection of Structural Variants in Targeted Sequencing

Live Webinar on Detection of Structural Variants in Targeted Sequencing

Structural Variants (SVs) have long been implicated in many human diseases such as cancer, making their detection important in clinical genomics. Strand NGS 2.5 includes a new workflow step for detecting these variants based on split reads that span the breakpoints corresponding to the variants. Detection of SVs using split reads provides breakpoints with a higher precision compared to the methods based on paired-end reads. In this webinar, we will describe this method and demonstrate its application to detection of somatic gene fusions in targeted sequencing data. We will also show how the detected SVs can be visually validated in the elastic genome browser of Strand NGS.

Speaker: Dr. Shanmukh Katragadda, Vice President – Software Technology, Strand Life Sciences

Register here: http://www.strand-ngs.com/webinar_registration

Date: 30 September 2015
Session 1: 2:00 PM IST (10:30 AM Berlin Time)
Session 2: 9:30 PM IST (09:00 AM PST)

Live Webinar on Calling narrow and broad peaks from ChIP-Seq data

Live Webinar on Calling narrow and broad peaks from ChIP-Seq data on 26 Aug 2015

In this month’s webinar, we will demonstrate and assess the algorithms in StrandNGS for both narrow and broad peak calling. Specifically, results from using ‘MACS’ algorithm for detecting the FOXA1 transcription factor binding sites and from ‘Find Enriched Regions’ approach for detecting histone H3K36 modification regions will be discussed.

Webinar details:
Session 1: 2:00 PM IST; 26 Aug 2015
Session 2: 9:30 PM IST; 26 Aug 2015
Register at http://www.strand-ngs.com/webinar_registration

Integrative RNA and ChIP-Seq analysis of regulatory T-cells

Integrative RNA and ChIP-Seq analysis of regulatory T-cells , a Strand NGS application note describes how integrated multi-omics functionality in Strand NGS was used to find the regulatory role of FoxP3 in T-regulatory and T-helper cells. Learn how the gene expression profiles from RNA-Seq and FoxP3 DNA-protein binding sites from ChIP-Seq are integrated. For mor information, please write to us

Integrated mRNA and microRNA transcriptome analysis in Strand NGS

Using a nasopharyngeal carcinoma case study, this paper highlights the integrated transcriptome analysis capabilities of Strand NGS demonstrating the identification of miRNA – mRNA interactions in regulatory networks.
Read the application note on Integrated mRNA and microRNA transcriptome analysis in Strand NGS by Veena Hedatale and Rohit Gupta. For more information, please contact us

Strand NGS-Calling narrow and broad peaks from ChIP-Seq data

Know about the state-of-the-art algorithms implemented in Strand NGS for detecting the binding sites of transcription factor (narrow peaks) and enriched regions of histone modification (broad peaks) from ChIP-Seq data.
Read the benchmarking study on Calling narrow and broad peaks from ChIP-Seq data in Strand NGS by Rohit Gupta and Anita Sathyanarayanan. For more information, please contact us

Strand NGS v2.5 Release Announced – Know what’s new in it?

Happy to share the release of Strand NGS v2.5. This release comes with many new exciting features and enhancements. Some of the major enhancements include new workflow for MeDIP-Seq analysis, split read alignment, new structural variant caller using split reads, additional RNA QC plots, enhanced RNA-Seq workflow to handle large-scale projects, correlation analysis, meta-data analysis, new and improved CNV visualisations (genome browser and web browser).

Additionally several enhancements are made with respect to visualizations and for high confidence variant calling. All these new features are available once you update the product by clicking on Update Product from the Help menu. For more information, please see the release notes. In case you need any assistance, please write to us at support@strandngs.com or sales@strandngs.com

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