NGSengine® Software

NGSengine is platform-independent software for the high-resolution identification of HLA alleles by Next Generation Sequencing (NGS).

NGSengine is IVD in EU/EEA, Switzerland, Norway, Turkey, South-Africa and Canada.

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Contact our technical support team at support@gendx.com

 

Instructions for Use

 

NGSengine® IFU ed. 8, CE

NGSengine® IFU ed. 8, RUO

NGSengine KIR Analysis IFU ed. 2, RUO

NGSignition IFU ed. 3, RUO

Protocol for allele submission to the GenBank

NGSengine Download and Updates

Please note that you need a valid license key to use the software.
Contact sales@gendx.com for information or request a free one month trial.

Latest version: NGSengine version  2.14 (22 July 2019)

 

Previous versions

Please note: The newest version of the software can be downloaded using the links above.

NGSengine version 2.13.1   [.msi file]
NGSengine version 2.12.1   [.msi file]
NGSengine version 2.11.1   [.msi file]
NGSengine version 2.10.2    [.msi file]
NGSengine version 2.9   [.msi file]
NGSengine version 2.8.1   [.msi file]
NGSengine version 2.7   [.msi file]
NGSengine version 2.6   [.msi file]

NGSengine release notes

 

NGSengine 2.14 release notes

New Features

Major

  1. A typing resolution optimizer is added. Optimized typing reports genotypes at a resolution level with the least amount of ambiguities. Optimized typing can be done at 4-field, 3-field, 2-field, P-group, and G-group level per allele, and can be exported in the PDF report and in the TARR file.
  2. New default button for loci analysis settings.
  3. New button for NGSgo-AmpX DRB1 All Exon loci analysis settings.
  4. Default analysis settings for DRB1 phasing have been changed from ‘cluster’ to ‘classic’.
  5. IMGT/HLA database release 3.36.0 is included and selected by default.
  6. NMDP and serology lists have been updated.

Minor

  1. The typing algorithm has been improved: in cases with many phasing regions the typing accuracy is improved as well as the performance.
  2. Quality trimming has been switched off for long read sequence data (ONT, PacBio).
  3. The review date in the .csv and .tsv exports has been adjusted to a region-specific format in digits.
  4. Extrapolation has been improved for HLA-B*40:83, HLA-C*15:05:06, DQB1*06:62, DQB1*06:240, DRB3*02:30, and KIR3DP1.
  5. A default ignore region was set for KIR2DS2 to exclude a homopolymer in analysis.
  6. The base variation plot in the overview tab has been enlarged.

Bug fix

  1. The ‘set as preferred’ option in the genotype ranking tab now ensures that remaining ambiguities are correctly included in the report.
  2. Fixed a bug where in certain conditions projects created by NGSserver could not be opened by NGSengine.
  3. Fixed a bug where samples that were unlinked after analysis resulted in a corrupted project.
  4. Small bugs have been fixed.

TARR update

  1. A few non-informative attributes have been discarded.

NGSengine passed all tests; no regression has been detected.

NGSengine 2.13.1 release notes

IMPORTANT NOTE: This release is a hotfix for NGSengine 2.13.0 

Bug fix

HLA-A*01:11N can now be typed correctly when using IMGT/HLA database 3.35.0.

NGSengine passed all tests; no regression has been detected.

NGSengine 2.13.0 release notes

IMPORTANT NOTE: projects opened with NGSengine 2.13.0 cannot be opened with NGSengine 2.12.1 or lower. 

New Features

Major

  1. Scrolling through the samples in the overview screen is now a joyful experience, because speed has increased.
  2. Approving and Rejecting results is now much faster.
  3. Samples that are grouped are now visible in different tabs on the overview screen.
  4. The “analyze” button changes to “analyze group” when groups are present, clicking this button will only analyze the samples in the active group.
  5. The filter works on all groups, and the number of filtered samples is also shown in the tab.
  6. The samples in the overview are now live filtered.
  7. The typing algorithm has been improved, resulting in better typing results for especially DPB1.
  8. In the genotype ranking tab you can select the resolution, which allows for fast inspection of second field ambiguities.
  9. IMGT/HLA database release 3.35.0 is included and selected by default.

Minor

  1. Samples in the overview are now alphanumerically sorted
  2. Extrapolation has been improved for DRB1*14:20, DRB3*02:07, DQB1*03:126, DQB1*06:74 and DQB1*06:62.
  3. The ignore region of HLA-B at the 3’UTR and the ignore region of DRB5 in intron 2 have been changed.
  4. The ignore regions of DRB1 have been reduced to include the splice sites in the analysis.
  5. The analysis region of DRB1 NGSgo-AmpX has been increased to allow for distinction between DRB1*08:01:01 and DRB1*08:77.
  6. Changing the library while analysing is no longer possible, which prevents library cache corruption.
  7. The dropdown menu with projects contains more projects, the latest one is the first in the list.
  8. The minimal read depth can now be set to 100.

Bug fix

  1. Check for license expiration has been improved.
  2. DPA1*01:03:01:05 will now be typed correctly.
  3. In the pdf report, Allele ambiguities are now also shown for the genotype ambiguities.
  4. Small bugs have been fixed.

NGSengine 2.12.1 release notes

Bug fix

  1. The element name “genotype” in “GenoTypeList” in the TARR.xml was changed to “genotypes” in 2.12.0, this has been corrected back to “genotype”.

 

NGSengine 2.12.0 release notes

New Features

Major

  1. The “Base Variation” plot can now be displayed in the alignment tab. This plot has been renamed from “Percentage most frequent base call versus rest”.
  2. Locus default settings for the new multiplex (NGSgo-MX6-1) can be applied with a single click.
  3. IMGT/HLA database release 3.34.0 is included and selected by default.

 

Bug fix

  1. The PacBio consensus read table is again visible in the Alignment tab.
  2. GLIMS export will be created even when there are over 1000 ambiguities.
  3. Small bugs have been fixed.

 

NGSengine 2.11.0 release notes

New Features

Major

  1. New advanced filtering options have been implemented. Filtering is now possible based on:
  • Sample name
  • Locus
  • Data quality
  • CWD status
  • Presence of mismatches
  • Analysis status
  • Review status
  • and more
  1. To draw attention to samples that need extra inspection, a warning will be shown when a locus with low quality data or exon mismatches is approved.
  2. IMGT/HLA database release 3.33.0 is included and selected by default.

 

Bug fix

  1. Extrapolation of HLA-A*02:156, DQB1*06:16, and DQB1*06:110 has been improved.
  2. Small bugs have been fixed

NGSengine passed all tests; no regression has been detected.

 Version 2.10.2 Release – 25 July 2018

 

Bug fix

  1. The pdf report of projects saved on a shared network drive include images again.

Installing version 2.10.2 is recommended for users who save NGSengine projects on a shared network drive.

NGSengine passed all tests; no regression has been detected.

 

NGSengine 2.10.1 release notes

Minor

  1. Removed splice site at exon4-intron4 of DRB3 from priority region.

Bug fix

  1. Samples with mismatches only in splice sites are now completely analyzed.
  2. The extrapolation for genomic intron 4 sequence for DRB3*03:01 turned out to be wrong and has been removed.

Reanalysis of DRB3 data in projects analyzed with NGSengine 2.10.0, where NGSgo settings were not used, is recommended.

NGSengine passed all tests; no regression has been detected.


NGSengine 2.10.0 release notes

New Features

Major

  1. The note introduced in NGSengine 2.9 has evolved into a comment. Comments can be created for a sample or a locus. They can be included in the personalised pdf report.
  2. The CWD status of alleles is shown on the overview screen, when the “Show CWD-info” is selected.
  3. HL7 version 2 can be exported.
  4. GL-strings are now included in the TARR export.
  5. IMGT/HLA database, release 3.32.0 is included and selected by default.

Minor

  1. When reviewing all loci of a sample, it is now possible to ‘undo all’ in one click.
  2. The mappability has been added to the quality parameters.
  3. In the alignment view, the user can filter the alleles shown in the alleles dropdown by entering part of the allele name.
  4. All splice sites have been added to the priority regions.

Bug fix

  1. The DPB1 insert size graph is now scaled around the insert size of the majority of the reads.
  2. Signatures are now shown correctly in the PDF report.
  3. The realignment algorithm has been improved for specific cases.
  4. Extrapolation of DQB1*06:20 has been improved.
  5. NGSengine no longer crashes when specific files are in a ‘read only’ mode.

NGSengine passed all tests; no regression has been detected.



NGSengine 2.9.1 release notes

Bug fix

  1. Known deletions were missing in the IMGT/HLA 3.31, e.g. in HLA-C*06:116N. This has been adjusted.

Minor

  1. Improved the customized tabular export performance.
  2. Added new C*07:02:01:17N null allele position to priority region.
  3. Defined core regions for KIR and MIC genes

NGSengine passed all tests; no regression has been detected.



NGSengine 2.9 release notes

New Features

Major

  1. Relevant allele ambiguities are reported more clearly in the PDF report.
  2. ‘Analysis’ reporting trigger is now the ‘Analysis & Review’ trigger.
  3. TARR exports are also generated when rejecting a sample.
  4. Improved alignment in HLA-B 3’UTR.
  5. MICA and MICB amplicon information and ignore positions have been added.
  6. IMGT/HLA database, release 3.31.0 is included and selected by default.

Minor

  1. A note can be added to each locus of a sample (this note only is available in the sample overview).
  2. ‘Custom’ PDF reporting profile is opened by default.
  3. Queued samples can be cancelled without delay.
  4. For various DQB1 and HLA-B alleles the extrapolation sources have been changed.
  5. Added a link to IMGT/HLA website in the help menu.

Bug fix

  1. In some rare cases ‘Prepare for submission’ resulted in incomplete sequences. This has been fixed.
  2. “Do not check for updates on startup”-checkbox is no longer disabled.
  3. Preview noise plot in the overview is correctly refreshed after accepting a working copy.

NGSengine passed all tests; no regression has been detected.

NGSengine 2.8.1 release notes

Bug fix

  1. Calculation of the delta signal-to-noise (∆SN) ratio in the quality metrics has been corrected.

Minor

  1. Saving of the project file is now more robust.

NGSengine passed all tests; no regression has been detected.

 

NGSengine 2.8.0 release notes

NGSengine obtained a Canadian Medical Device License on the 10th of July 2017, authorizing its diagnostic use in Canada.

New Features

Major

  1. NGSengine® now reports ‘Quality Metrics’ in the overview screen.
      a. Quality metrics are available for Amplicon, Exon+ region, Core+ region or a combination of these regions.
      b. Quality metrics can be selected by a drop-down menu in the overview screen.
      c. Intermediate quality values are shown in yellow, low-quality values are shown in red.
      d. Quality threshold settings can be set through File>Preferences>Quality Thresholds.
      e. Default settings for the quality thresholds are available for different platforms and per region.
      f. The advanced filter option allows for selecting results based on quality.
      g. Quality metrics can be exported through File>Export >Metrics report and by using the Custom export.
      h. Quality metrics are present in the TARR.xml file.
  2. Hovering over a new icon next to the locus shows the ‘Percentage most frequent basecall versus rest’ plot for easy inspection.
  3. Reporting genotype ambiguities with intron mismatches can be selected in the settings: File>Preferences>General.
  4. Mismatches found in extrapolated regions are indicated by an orange line underneath the exon and/or intron mismatches.
  5. Mismatches in extrapolated regions are indicated with an orange box in the genotype ranking tab.
  6. The latest IMGT/HLA database, release 3.30.0, is included and selected by default.

Minor

  1. Using the “Previous/Next” buttons in the alignment tab shows the (filtered) loci as shown in the overview screen.
  2. The option 'Always show reads' is once selected becoming default when opening.
  3. The File>Export menu has been redesigned.
  4. The customizable export through File>Preferences>Exporting has been redesigned for the tab/comma separated value files.
  5. NMDP codes are now present in the TARR.xml.
  6. Several priority regions have been added to distinguish Null alleles from expressed alleles and to cover intron splice sites.
  7. Extrapolation of several alleles - with yet unknown sequence in the IMGT/HLA database - has been improved.
  8. Core regions of non-HLA genes have been defined.
  9. The TARR schema (.xsd) file has been updated on the website.
  10. The overall performance has been improved.

Bug fix

  1. The auto-amplicon finder has been repaired.
  2. The ambiguities list in the tabular export now shows the possible genotypes with the exact same number of exon and intron mismatches.
  3. The number of P-group genotypes is now correctly shown.

NGSengine passed all tests; no regression has been detected.

NGSengine 2.7.0 release notes

NGSengine obtained a Canadian Medical Device License on the 10th of July 2017, authorizing its diagnostic use in Canada.


New Features
Major

  1. Insertions not present in the IMGT/HLA database are now reported (Illumina and Ion Torrent only).
           a.  A warning will be shown in the overview.
           b.  The typing result will be shown in orange/red.
           c.  The statistics tab includes an additional ‘Insertions’ plot.
           d.  Detected insertions are mentioned in the report.
           e.  A new entry has been created in the TARR file.
  2. A pdf report of a single sample can be generated with a right click option in the overview screen. Selecting multiple samples followed by this right click option results in generating a separate pdf for each selected sample.
  3. A realignment step has been added to the analysis to improve the alignment of read ends. This results in a decrease of noise in specific regions.
  4. The latest IMGT/HLA database, release 3.29.0, is included and selected by default.

Minor

  1. The tabular export can now be extended to include ambiguities, P-groups and G-groups.
  2. The TARR also includes the typing result for two fields, three fields, P- and G-groups.
  3. Loci that are detected but not analyzed are removed from the pdf report.

Bug fix

  1. Fourth field typing in DPB1 has been improved by resolving an alignment issue in a repeat region.
  2. NMDP code assignment for DPB1 has been improved.

NGSengine 2.6.0 release notes

New Features

Major

  1. The second reviewer has options to review/edit the data, enabling re-analysis using different settings or applying edits, before approving or rejecting.
  2. In the overview screen, the user can toggle between gDNA, cDNA and/or codon numbering.

It is also possible to ‘jump’ to a cDNA position or a codon.

  1. The user can reallocate the data folder in case it has been moved.
  2. The file with user login credentials can be stored on a network location which makes it possible to log in from any network connected computer with NGSengine.
  3. The user can adjust the lower threshold for heterozygosity detection, facilitating allele detection in samples with unbalanced alleles.
  4. IMGT/HLA database, release 3.28.0 is included and selected by default.

 

Minor

  1. The desktop icon has been changed.
  2. The TARR also includes the typing results for two and three fields and P and G groups.
  3. Loci DRB2, DRB8 and DRB9 are now included in the IMGT/HLA.

 

Bug fix

Trying to save a pdf report when it is opened will no longer cause a crash.

NGSengine 2.5.1 release notes

Bug fix

This issue is only applicable for HLA-DQB1 whole gene analysis in combination with IMGT/HLA database 3.27.0.

       1. The extrapolation of exon 5 for some DQB1 alleles has been corrected.

NGSengine 2.5.0 release notes

New Features

Major

  1. PDF reports can be customized:
    I.    Select which paragraphs and typing information should be included in the report.
    II.   Define the order of sections in the report.
  2. New allele submission: files can be generated needed for a submission to GenBank.
  3. For PacBio consensus reads, it is now possible to select which consensus reads will be used for analysis.
  4. The user can select which loci should be analysed, only detected or ignored, through the preferences window.
  5. Beside the classical HLA genes all other IMGT/HLA loci are available for analysis, which can be unlocked with a special license.
  6. IMGT/HLA database, release 3.27.0 is included and selected by default.

 

Minor

  1. ‘Ask for support’ email has been adapted.
  2. The warning system for HLA-DRB loci has been improved.
  3. When a project is locked by another user, NGSengine will indicate which computer and user has the project currently open.
  4. In the TARR export files, DRB3, DRB4 and DRB5 are now displayed as single genes, instead of a homozygous genotype.
  5. The TARR export files now includes the genotype ranking list.
  6. Performance of exporting mechanism has improved.

 

Bug fix

  1. Licensing process has been improved greatly.
  2. Jump to next mismatch now also works when smaller regions (e.g. Exons+/Core+) are selected.

NGSengine 2.4.0 release notes

New Features

Major

  1. Serologically defined antigens have been added to the report, export and genotype ranking list
  2. The question marks in the overview screen are colored according to their position
  • Red when there is at least one question mark in a core+ region
  • Black when there is at least one question mark in an exon+ region outside the core region
  • Grey when there are only question marks in introns or UTRs
  1. In the alignment overview, two buttons are added, enabling easy jumping to the previous or next question mark or mismatch.

 

Minor

  1. It is now easier to switch between IMGT libraries when you want to inspect a locus that has been analysed with another IMGT library.
  2. The xml tab now contains the locus specific information of the total analysis results (TARR) xml
  3. The typing xml export has been discontinued
  4. DRB3, 4 and 5 are now also shown as a single allele in the pdf report.

 

Bug fix

  1. Some small bugs have been fixed

NGSengine 2.3.0 release notes

New Features

Major

  1. IMGT/HLA Database, release 3.26.0.1 is included and selected by default
  2. Microsoft .Net 4.6.1 framework is mandatory to run NGSengine®
  3. HLA-DRB locus:
    - Indication of expected DRB3, 4 or 5 gene presence is based on obtained DRB1 typing result.
    - A warning is shown in case of unexpected presence or absence of DRB3, 4 or 5.
    - These alerts can be enabled or disabled via the preferences.
    - HLA-DRB3, 4 and/or 5 are now shown in the overview, report and export as a single allele; i.e. DRB5*01:01:01 instead of DRB5*01:01:01, DRB5*01:01:01
  4. Typing resolution:
    - Typing results can be presented as Full Resolution, 3 fields, 2 fields, P or G groups in the overview.
    - P and G groups are also included in the genotype ranking list, reports and export files.
  5. In the overview the message "Insufficient data" is shown in case the core regions are not completely covered.
  6. Additional filtering options; on locus, number of exon/intron mismatches, question marks, and more.
  7. Typing of third party supplier HLA-DRB1 amplifications is improved by enabling of pseudo gene detection during analysis, for now only HLA-DRB6 is included.

Minor

  1. In case of genotype ambiguities, the genotype ranking list is collapsed.
  2. For sample files derived from Illumina platform the "_S" with a number is removed from the sample name. This can be changed in the preferences.
  3. Sample files with specific naming; such as "Undetermined_" or "Empty" can be ignored.
  4. The default location of a new project is the folder of the last opened project.
  5. The noise plot in the statistics window has been improved.
  6. The minor base frequency graph has been disabled.
  7. The sequencing platform is detected automatically, and can be changed by the user.

Bug fix

  1. Several small bugs have been fixed, amongst others in the report.
  2. Typing for HLA-B*35 and HLA-B*51 has been improved by ignoring some positions in the 3'UTR region of HLA-B.
  3. Offline activation is possible on all computers

 

NGSengine 2.2.0 release notes

New Features

Major

  1. IMGT/HLA Database, Release 3.25.0, 2016-07-14 is now included and is selected by default.
  2. It is now possible to limit the analysis region to Exon+ or Core+ region(s) via the preference menu.
    - Core+ region view is added to the alignment view.
  3. Number of undetermined homo-heterozygous positions is now presented on the overview screen, in the alignment view, and the export files.
  4. Typing accuracy:
    - Intron analysis has been improved.
    - DPA1*01:05 typing is no longer affected by missing IMGT data.
    - Typing of certain null alleles (e.g. DQB1*02:20N) has been improved.
    - DRA and HFE can now be analysed, and are available in an extended IMGT database.
  5. The support options have been improved to facilitate sharing of data.
  6. PDF reports can now be generated per analysis group.

Minor

  1. It is now possible to export the sequence and names of individual reads.
  2. Improved validation of Fastq files.
  3. Performance improvements for PDF report creation.
  4. Several optimizations in LIMS exporters.

Bug fix

  1. Errors when reading of .gz-files no longer occur.
  2. Genotypes are now always presented in the correct order.
  3. Settings can now be adapted for non-core genes (e.g. MICA).
  4. ‘BLAST this sequence’ points to updated NCBI URL.

 

 

NGSengine 2.1.0 release notes

New Features

Major

  1. IMGT/HLA Database, Release 3.24.0.1, 2016-05-04 is now included and is selected by default.
  2. As of IMGT/HLA Database Release 3.24.0.1, DRB3, DRB4 and DRB5 genes are now analysed as separate genes, improving the typing accuracy for all HLA-DRB genes.
  3. Under certain conditions, manual editing is now possible:
    - Status of a single nucleotide position can be changed from homozygous to heterozygous or vice versa.
    - Single nucleotide positions can be ignored or included in the analysis.
    - Under certain conditions, non-phased regions can be phased or phasing can be broken.
    - Preferred allele can be indicated and order in listing will be affected accordingly.
  4. All manual changes are presented in the reports.
  5. Typing accuracy has been improved, in particular for DQA1*04:01 and HLA-C*04:82 alleles.
  6. Analysis of certain intronic regions have been optimized.
  7. Analysis time has been shortened.

Minor

  1. Project names are now included in the reports.
  2. Short freeze during the saving step no longer occurs.
  3. Options for analysing NGS projects generated with third party workflows have been extended.

Bug fix

  1. Long allele names are now completely readable in the alignment view.
  2. All phasing lines are now presented correctly.
  3. Approval comments are now also visible in the locus report.
  4. Locus names in some LIMS exporters have been adapted.

NGSengine Release Certificates

To assist you with your institute's quality coordination process, we are pleased to provide you the with NGSengine® Release Certificates:

2019

   Version 2.14, July 22, 2019

    Version 2.13.1, June 20, 2019

Version 2.13.0, March 19, 2019

Version 2.12.1, February 1, 2019

2018

  Version 2.12.0, December 17, 2018

  Version 2.11.0, September 24, 2018

   Version 2.10.2, July 25, 2018

  Version 2.10.1, July 23, 2018

Version 2.10.0, July 16, 2018

Version 2.9.1, April 19, 2018

Version 2.9, April 5, 2018

Version 2.8.1, February 26, 2018

Version 2.8.0, January 11, 2018

2017

Version 2.7.0, October 4, 2017

Version 2.6.0, June 21, 2017

Version 2.5.1, Apr 25, 2017

Version 2.5.0, Mar 15, 2017

2016

Version 2.4.0, Dec 19, 2016

Version 2.3.0, Dec 5, 2016

Version 2.2.0, Sept 7, 2016

 Version 2.1.0, June 9, 2016

Version 2.0.0, Feb 18, 2016

2015

Version 1.10.1, Dec 7, 2015

Version 1.10, Nov 23, 2015

Version 1.9, July 28, 2015

Version 1.8, Apr 15, 2015

2014

Version 1.7, Dec 11, 2014

Version 1.6, Oct 15, 2014

Version 1.5, July 11, 2014

Version 1.4, Apr 29, 2014

 Version 1.3, Feb 6,  2014

2013

Version 1.1, Oct 24, 2013

 

NGSignition Release Certificates

To assist you with your institute's quality coordination process, we are pleased to provide you the with NGSignition® Release Certificates:

  Version 2.12.0, Dec 17,  2018

 

end faq

 
 

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