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上传时间:2017-06-02 16:37:10
Version: v3.0
Release Date: 4-Apr-2017


New Features / Enhancements:
1. DNA-Seq is now faster and more accurate. Whole exome and genome precision and recall rates are comparable to GATK best-practices workflow, while being twice as fast. Important changes are:
DNA alignment:
a. Mapping quality logic has been changed. Now the mapping qualities range from 0 to 70 and they better represent the quality/uniqueness of mapping.
b. Noisy ends are now soft clipped. This has improved the downstream steps like local realignment and SNP detection.
c. Dynamic programming (DP) step has been optimized for speed.
d. Penalties used in dynamic programming (DP) have been changed to be in line with other tools in the industry. For more details please check Tools -> Options -> Alignment -> Mismatch/Gap penalties.
e. When split alignment option is selected, large gap alignment is performed first and then split alignment is attempted on unaligned reads. This improves the detection of longer InDels.
Local realignment:
f. Local realignment has been significantly improved.
SNP detection:
Following new parameters have been introduced in Tools -> Options to improve the precision of variant calls:
g. Ignore reads with mapping quality less than
h. Ignore reads with tail distance less than
i. Ignore split reads and partial reads
Pipeline:
j. A new pipeline - "Strand NGS Best Practices - Detect SNPs" has been packaged. This pipeline provides a simple way to identify variants with high precision and recall.
2. HGVS notation columns have been added to SNP Effect analysis output. Genomic HGVS, cDNA HGVS and Protein HGVS are the new columns that have been added.
3. RNA alignment has been optimized for speed. Now transcriptome alignment runs two times faster. Other alignment options too have similar speed gains. Important changes are:
. Dynamic programming step has been optimized by taking advantage of Intel's SSE (Streaming SIMD Extensions).
a. File I/O has been optimized.
4. In ChIP-Seq, a new plot - TSS plot has been added. Transcription Start Site (TSS) plot displays read densities from all the samples in respect to Transcription Start Site and the specified upstream and downstream regions.
5. SNP detection wizard is self contained now. All parameters from Tools -> Options -> DNA Variant Analysis -> SNP Detection have been brought into the wizard. With this change every invocation of SNP detection is insulated from changes done to tools-options while it is running.
6. Check for known variants workflow has been made a background job. It can now be added to a pipeline. Also additional quality columns have been added to the output (average base, mapping and alignment qualities).
7. Adapter trimming has been made more robust by detecting external dependencies like python during the wizard step itself.
8. Methylation detection has been optimized for speed.
9. A new demo DNA experiment (chromosome 21) and associated annotations have been added to the demo project that is packaged with the tool.
10. Pipeline manager wizard has been enhanced to choose the project for adding newly created experiment.
11. UI improvements:
. A new home screen (launch screen) has been implemented. This screen gives quick access to common tasks like running pipelines, opening recent/existing projects, reading technical literature and opening demo project.
a. SNP filters list (in SNP filter manager) and pipelines list (in pipeline manager) can now be dynamically searched. This is very useful for cases with large number of entries in the list.
b. Pipeline graph can now be exported as an image from the pipeline manager.
c. In MOA correlation analysis, UI has been enhanced for the Sample/Condition pairing page. In this page it is now possible to sort individual columns, which comes in handy when pairing large number of samples.

Bug Fixes:
1. Base-composition-by-position plot was missing the legend. This has been fixed
2. SNP multi-sample-report was containing dbSNP format entries. This has been fixed
3. For large samples with more than 2 billion reads, the raw sample inspector was showing negative number of reads. This has been fixed
4. Targeted CNV was failing with contamination correction in some cases. This has been fixed
5. Exporting variants in a targeted DNA-Seq experiment was failing. This has been fixed
6. In RNA-Seq experiments with multiple samples, partition counts plot in gene view was blank. This has been fixed.
7. Gene view was blanking out after hiding sidebars. This has been fixed.
8. Extract relations via NLP was not working. This has been fixed
9. Annotation manager related:
a. In gtf file import some of the transcripts were missing. This has been fixed
b. Importing a build with more than 500 sequences caused the tool to freeze randomly. This has been fixed
c. Disk space check done during annotations import has been cleaned up to better handle the cases of changing repository location and temporary folder location.
10. Server related:
a. RNA alignment was failing with uploaded local samples. This has been fixed.
b. User level temporary folders on the server were not cleared upon server or client restart. This has been fixed.