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上传时间:2016-09-30 09:39:40
Version: v2.0
Release Date: 2-July-2014


We are happy to announce the release of version 2.0 of Avadis NGS under a new name 'Strand NGS'. It combines enhancements to Avadis NGS with unique features from the Agilent Technologies’ GeneSpring® NGS module, through the addition of a Methyl-Seq workflow, direct access to BioCyc and WikiPathways, better support for targeted sequencing experiments and Multi-Omic Pathway Analysis. Here are the details of the additions in v2.0.
New Features / Enhancements

1. A new workflow for the analysis of bisulfite-treated methyl-seq data has been included. Most of the methods that have been developed to determine the methylation status of the genome typically rely on one of the two approaches: bisulfite conversion or a form of methylated DNA enrichment. The Methyl-Seq Analysis workflow in Strand NGS supports analysis of bisulfite-converted reads from a whole-genome, targeted sequencing, or an RRBS experiment. It allows detection of methylation at base pair resolution in individual samples. It also facilitates finding differentially methylated cytosines across conditions, and identification of the genic regions affected by the methylated bases. Further downstream analysis such as GO, and pathway analysis can be performed on the set of affected genes. QC plots and visualization specific to methyl-seq data have been provided to aide the analysis.

2. Special support for the analysis of targeted sequencing data has been provided. The experiment creation wizard has been enhanced to take the set of targeted regions corresponding to the 'Targeted Sequencing Kit' as an additional input, and to produce special QC plots and metrics that help in evaluating the quality of the targeted sequencing data. These plots are available as 'Target Enrichment QC' in the new 'Quality Control Manager' under the Quality Inspection section of the workflow. This support for targeted sequencing is available for RNA-Seq, DNA-Seq, and Methyl-Seq experiments.

3. The various QC plots and metrics in the analysis experiments have been consolidated into a single workflow step called 'Quality Control Manager' to facilitate easy access. These include, in addition to the already existing pre-alignment and post-alignment QC plots, a new set called 'Library QC' which provides metrics that pertain to the sequence library. Library QC helps to determine if all the regions are represented in the sequence library and that there is no redundancy. In case of targeted sequencing applications, the QC Manager also shows the metrics related to target enrichment. Note that the QC Manager is present only in the analysis experiments, and the alignment experiments continue to have the QC plots as multiple workflow steps as earlier.

4. Annotations Manager has been enhanced to show all the annotations for a build in a folder structure based on their feature type. Also, the annotations that have been so far called 'Target Regions' are renamed as 'Regions of Interest' in order to differentiate from 'Targets' which are the new type of annotations used to represent the regions from targeted sequencing kits

5. Pathway analysis has been enhanced by providing access to WikiPathways and BioCyc pathways. The tool can now download WikiPathways from the WikiPathways web page directly, whereas BioCyc pathways are made available on the Strand NGS server for download via Annotations Manager. It is also possible to import pathways in BioPax (Level 2 or 3) or in GPML format. Also, there have been some changes to the names of the workflow steps related to pathways analysis - 'Find Significant Pathways' has now become 'Single Experiment Analysis', and 'Launch IPA' is now 'Export to IPA'. 'Multi-Omic Analysis' is a new step that allows integration of results from different experiment types and multiple organisms, and to visualize experimental data overlaid on curated pathways or literature derived networks.

6. Support for running GSEA analysis on oncogenic signature (C6) and immunologic signature (C7) gene sets has been added.

7. An updated version of the Gene Ontology data has been packaged with the tool. Also, the interaction databases on the Strand NGS server have been updated with literature upto Sep 2013.

8. Plot views and pathways including matched pathway lists can now be exported as a pdf report or saved locally in the navigator. These reports can be created with customized formatting. Multiple reports can be merged to create a single report.

Bug Fixes:

1. SNP effect analysis on imported Variant Allele Lists (VALs) would fail in some cases. This has been fixed.

2. Local realignment would fail in some rare cases while handling hard clipped reads. This has been fixed.

3. SNP Effect Analysis would fail in case of incorrect annotations containing transcripts for which the CDS start or end falls outside the exon boundaries. This has been fixed by excluding such transcripts from the analysis.

4. Exporting SNP list in VCF format would fail in some corner cases such as a deletion and insertion occurring next to each other. This has been fixed.

5. The region lists folder created by the local realignment step that contains the lists of realigned regions would become inaccessible after closing and relaunching the tool. This has been fixed, and such a thing will not happen with the results created in the new version of the tool. However note that the inaccessible results from the previous version will remain so.

Known Issues:

1. SV detection would give incomplete results occasionally due to some issue in multi-threading. Hence multi-threading has been turned off to ensure the completeness of the results.

2. When the input to the Region List Operations is an annotation (such as the region list under the Targets folder in the navigator, or an annotation added to the experiment through the 'Search' menu), saving of the result is not possible.

3. In small RNA experiments, hyperlinks shown in the entity list inspector do not work.