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上传时间:2016-09-30 10:42:37
Version: v2.7
Release Date: 02-Jun-2016


New Features / Enhancements:

Strand NGS v2.7 is upgraded to work with Java 1.8 and now also supports Mac OS X El Capitan.

"Target Region QC" and "Combining multiple RNA-Seq analysis experiments" steps have been optimized to significantly reduce their running time.

A new SNP caller "Low Frequency SNP Detection" has been introduced. It uses a modified binomial approach to account for base qualities and has the ability to detect low-frequency SNPs. Hence this method can be a preferred choice for detecting somatic mutations and variants in non-diploid organisms.

Alignment of circular genomes is now supported through enhancements to split alignment feature.

A script is provided to create and save a subset of the dbSNP database based on the target regions of interest. This typically much smaller subset can then be used to annotate the SNPs in all the consequent analysis runs. Hence depending on the size of the target panel, this feature is expected to reduce the SNP annotation time by ~95%. Further the script is generic enough to work with any VAL. 

In DNA-Seq workflow, "Find Damaging NS Variants" feature has been enhanced to include new version of the dbNSFP database, which includes predictions from new algorithms like MutationAssessor, FATHMM, MetaSVM and MetaLR; allele frequency information from additional sources like ExAC and ESP in addition to 1000 genomes; and new filtering option using conservation scores from phastCons.

An additional pre-processing step "Split Read Realignment" has been added in the DNA-Seq workflow to realign some of the poorly aligned reads. This pre-processing step can realign partially aligned split reads and noisy normally aligned reads using the evidence from other fully split reads in the region. This can enhance the support of true but low-frequency Structural Variant (SV) events.

DNA alignment algorithm has been enhanced further. Specifically, following improvements have been introduced:

Calculation of insert length for paired-end reads has been improved by considering only those uniquely matching read pairs which have single optimal match.

In case of paired-end read alignment, split alignment is now performed after mate rescue step.

After BWT search, duplicate seeds are removed from the list of top seeds.

A read is now split aligned if the cumulative alignment score of the candidate split fragments passes the threshold. This is in contrast to the previous logic, in which a pair of candidate fragments are considered split only if each of them separately pass the score threshold.
   
Local realignment has been enhanced. A user-defined parameter has been introduced in Tools → Options to ensure that only those InDels that are not near the start/end of the read are considered. Further haplotypes with invalid CIGAR (like *2I2D*) are discarded from the list of candidate haplotypes.

In earlier versions, SNP filters were only applied to Single Base Variants (SBVs), however the same SNP filters can now be applied to Multi Base Variants (MBVs) also. This can significantly reduce the number of false positive MBVs.

To reduce the number of MBVs reported, only top two based on supporting read % threshold are reported in germline SNP detection and all MBVs satisfying a supporting read % threshold are reported in low frequency SNP detection.

Export VCF functionality now also supports exporting SVs obtained using split reads in addition to exporting SVs from paired-end reads.

Similar to the import of region list, now "Import Entity List" and "Import VCF" functionality also gives the number of entities/variants imported out of the total number in the input file.

The notes section seen on inspecting the aligned read list has been enhanced to include mismatch/gap penalties and estimated mean/std of the insert length.

Sample can now be downloaded in either SAM or BAM format using the right click menu on the sample. Earlier only SAM format was available.

In genome browser bookmark location, now tab delimited search string (with chr, start, end) can be provided.

Bug Fixes:

In the methylation detection and DMR workflow steps of MeDIP-Seq experiment, if the interpretation doesn't have "Type" parameter, the tool would throw an exception. This is fixed by showing an appropriate error dialog display.

In ChIP-Seq experiment, sometimes the detected motifs are missing from the results upon restarting the tool. This has now been fixed.
Exporting the Variant Support View (VSV) image would export a png image but names it as '.jpeg'. This will not allow the exported image to open by default. This has been fixed now.

In some rare cases, alignment score of a read would go beyond 100. This has been fixed by computing the alignment score directly from CIGAR instead of NM tag.

In elastic genome browser, split read segments with soft clipped bases are not connected. This has been fixed.

Local Realignment may fail sometimes if there is an overlap of insertions and deletions. This has now been fixed by constructing two separate haplotypes, one for insertion and other for deletion.

To compute support for each haplotype in Local Realignment, all reads spanning the realignment region are considered. This has been fixed by computing the support using only the reads spanning the haplotype. In addition, the parameter 'supporting read % for haplotype' has been dropped from Tools → Options.

In Local Realignment, few valid candidate regions may be skipped because mismatch condition will only be checked to the left and right of the InDel boundary. This has now been fixed by checking for the mismatch condition in the entire stretch, including with in the InDel boundary.

The alignment score for small percentage of reads that are locally realigned would be wrong and may cause problems in downstream filtering steps. This has been fixed.

One of the advanced quality parameters, "Average Base Quality" of the detected SNPs would be wrong if soft-clipped reads overlap with the SNP location. This has been fixed now.

For some variants in the Multi-Base Variant (MBV) list, complex will be called as substitution and vice-versa. This has been fixed.

In the "Replicate Analysis" workflow step of RNA-Seq analysis experiment, Mann-Whitney unpaired test with Benjamin-Hochberg multiple hypothesis correction method may give inconsistent results on the linux platform because of undefined p-values for few genes. This has been fixed by discarding the genes with undefined p-values.

In some cases, even after RNA alignment job fails, jobs monitor would continue to show it running. This has been fixed.

In RNA alignment experiment with multiple samples, adapter trimming notes would only give information on the last sample processed. This has been fixed and now adapter trimming notes for all the experiment samples will be displayed.

In the SNP detection wizard, going back and forward would reset the SNP filters to default. This has been fixed.

While importing a region list using the "Import Region List" functionality, sometimes the last region is not imported. This has been fixed.

Some of the inconsistencies with # of transitions, # of transversions, and # of het/hom in the SNP summary statistics have now been resolved.

The filters on the genome browser read track may show inconsistent drop-down value when second filter is added. This inconsistency has been resolved.

Updating proxy server settings in Tools → Options would not take effect. This has been fixed.

The notes of the filtered read list object will show incorrect number of filtered reads if duplicate filter is used. This has been fixed.

In MeDIP-Seq experiment, single experiment analysis (SEA) with in pathway analyis workflow would fail. This has been fixed.

Inspecting an empty entity list would fail and throw uncaught exception. This has been fixed by disabling inspection on empty entity lists.