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上传时间:2016-09-30 10:48:16
Version: v2.8
Release Date: 23-Aug-2016


New Features / Enhancements:

1. Support for aligning genomes larger than 4 billion bases has been added.

2. Whole genome CNV detection has been optimized. It'll run faster and use lesser amount of memory. It can handle large samples.

3. Search functionality has been added to the region list inspector.

4. A 'Select All' checkbox has been added to the project export dialog enabling single click to select all the experiments.

5. For imported samples having coverage in X and Y chromosomes, Y/X ratio value has been added as an annotation to the sample. This annotation will be useful while performing any gender based analysis.

6. Logging has been enhanced to collect more job level information for quicker diagnosis of user issues.

7. Caching system has been optimized for smoother operation of the tool especially for long running jobs and extended usage of the tool without exiting.

8. Find significant SNPs, find somatic variants and create coverage profile workflow wizards have been optimized for quicker launch time.

9. Sample import has been optimized to handle samples containing reads from sequences which are not part of the build. Such reads will be dropped.

10. During low memory situations, usage of disk as swap space has been optimized. When working with large samples, several analysis tasks like SNP detection, local realignment, split read realignment, gene fusion, quantification and read list filtering would run faster.

11. An option has been added to tools-options menu to enable fixed trimming after adapter trimming. Default order is to do fixed trimming first and then adapter trimming.

12. VCF import has been optimized to handle large VCF files.

Bug Fixes:

1. On Windows 10, Strand NGS 2.7 was not installing. This issue has been fixed.

2. In SNP detection, when calculating additional confidence quality scores, qualities of hard-clipped bases were considered because of which SNP detection fails for reads with hard-clipped bases. This issue has been fixed.

3. Because of chromosome name differences between input sample and the experiment's build (like ChrMT and ChrM), some of the SNPs/SVs were not reported. This issue has been fixed.

4. Pre-packaged SNP filter SB50TR100 contained an incorrect "Strand Bias PV4" condition. This has been replaced by "Percent Strand Bias" condition.

5. SNP Detection with dbSNP fails when working with more than 500 samples. This has been fixed.

6. After doing some region list operations on a SNP region list and exporting the resultant region list as VCF, the exported VCF file contained incorrect header. Because of this, conversion of the VCF file to external formats like .gds was failing. This has been fixed.

7. SNPs in chromosome Y or mitochondria were reported as diploid in GT (genotype) tag in the exported VCF file. This has been fixed. Now they are reported as haploid.

8. Pre-packaged script to merge single base (sbv) and multi base (mbv) variants region lists was failing when the region lists contained empty values for dbSNP id column. This has been fixed.

9. In genome browser, while merging the coverage tracks a common ruler has been introduced. This fixes the issues of each of the merged tracks showing in its own scale and ruler label truncations. Now ruler is always enabled irrespective of the number of tracks merged (earlier it was only with two tracks).

10. Project export failures were not shown to the user. So the user was under the impression that the project export succeeded. This has been fixed.

11. Without genes and transcripts annotation, PICS peak detection was failing. This has been fixed.

12. When adding genes and transcripts from gff3 file, last gene was not getting imported. This has been fixed.

13. On Windows, alignment continued despite failure of adapter trimming. This has been fixed.

14. In the split read realignment logic, soft clipped bases were considered when determining if read end was noisy. This has been fixed by not considering soft clipped bases.

15. During local realignment, indels near the realignment region boundary could cause array index out of bounds exception when aligning a new read. This was because of not having reference bases for enough range outside the realignment region. This has been fixed.

16. Some workflow steps were creating empty output nodes even if there was no data. This has been fixed.

17. Correlation analysis was failing when running without selecting entity list. This has been fixed.

18. RNA alignment with novel splices fails for paired end data if one of the mates has zero length. This may happen during adapter trimming and has been fixed.

Known Issues:

1. On Mac OS X, small RNA quantification fails if 'Detect novel Small RNA genes' option is selected.