Bionano Solve v3.0.1 Release Notes

Transcription

1 Bionano Solve v3.0.1 Release Notes Document Number: Document Revision: B For Research Use Only. Not for use in diagnostic procedures. Copyright 2017 Bionano Genomics, Inc. All Rights Reserved.

2 Table of Contents Legal Notice... 3 Bionano Solve Revison History... 4 Bionano Solve Updates History... 4 Introduction... 5 References... 5 RefAligner... 5 Improvements... 6 Bionano Solve Pipeline... 6 SVMerge... 6 Hybrid Scaffold... 7 SMAP-to-VCF Converter... 7 Variant Annotation Pipeline (beta version)... 7 Known Issues and Limitations... 8 Technical Assistance Rev B, Bionano Solve v3.0.1 Release Notes Page 2 of 9

3 Legal Notice For Research Use Only. Not for use in diagnostic procedures. This material is protected by United States Copyright Law and International Treaties. Unauthorized use of this material is prohibited. No part of the publication may be copied, reproduced, distributed, translated, reverse-engineered or transmitted in any form or by any media, or by any means, whether now known or unknown, without the express prior permission in writing from Bionano Genomics. Copying, under the law, includes translating into another language or format. The technical data contained herein is intended for ultimate destinations permitted by U.S. law. Diversion contrary to U. S. law prohibited. This publication represents the latest information available at the time of release. Due to continuous efforts to improve the product, technical changes may occur that are not reflected in this document. BioNano Genomics reserves the right to make changes in specifications and other information contained in this publication at any time and without prior notice. Please contact BioNano Genomics Customer Support for the latest information. BIONANO GENOMICS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL BIONANO GENOMICS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT BIONANO GENOMICS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. Patents Products of Bionano Genomics may be covered by one or more U.S. or foreign patents. Trademarks The Bionano Genomics logo and names of Bionano Genomics products or services are registered trademarks or trademarks owned by Bionano Genomics in the United States and certain other countries. Bionano Genomics, Irys, IrysView, IrysChip, IrysPrep, IrysSolve, Saphyr TM, Saphyr Chip TM, and Bionano Access TM are trademarks of Bionano Genomics, Inc. All other trademarks are the sole property of their respective owners. No license to use any trademarks of Bionano Genomics is given or implied. Users are not permitted to use these trademarks without the prior written consent of Bionano Genomics. The use of these trademarks or any other materials, except as permitted herein, is expressly prohibited and may be in violation of federal or other applicable laws. Copyright 2017 Bionano Genomics, Inc. All rights reserved Rev B, Bionano Solve v3.0.1 Release Notes Page 3 of 9

4 Bionano Solve Revison History Revision Revision A Revision B Notes Initial release of document. Update added Bionano Solve Updates The following updates have been made to the 3.0 release of Bionano Solve. Update Change Ticket v [RefAligner] optarguments xml file update to turn on the MaxIntensity filter for Irys data and to disable memory "display" options; BIOIN-340 [Pipeline] Added -TotalThreads to apply on all jobs in optargs BIOIN Rev B, Bionano Solve v3.0.1 Release Notes Page 4 of 9

5 Introduction This document describes the release of Bionano Solve v3.0. In this document, we provide an overview of the fixes and improvements as they impact RefAligner, the Bionano Solve Compute pipeline, SVMerge, the VCF converter, the Hybrid Scaffold pipeline, and the tertiary analysis pipeline (beta version). Note: Bionano Solve v3.0 supports both the Saphyr and Irys instruments. Note: Bionano Solve v3.0 is only supported by Bionano Access. IrysView is not supported. References Visit for format specifications on the following files: BNX XMAP CMAP SMAP Bionano BED SVMerge Hybrid Scaffold Conflict Cut Status Structural Variant Annotation Pipeline RefAligner Added translocation confidence scores. Added translocation flagging (masking) based on input BED file entries with types "common" and "segdupe." Added zygosity classification for translocation breakpoint calls. Added output for all three components of raw confidence for insertion and deletion calls in SMAP output (for use in SVMerge). Modified parameters for Irys-specific XML files: Haplotype-aware assembly parameters for SV detection applications. Non-haplotype-aware assembly parameters for hybrid scaffolding applications. Added parameters for Saphyr-specific XML files: Haplotype-aware assembly parameters for SV detection applications. Non-haplotype-aware assembly parameters for hybrid scaffolding applications. Human-specific assembly parameters. Non-human specific assembly parameters Rev B, Bionano Solve v3.0.1 Release Notes Page 5 of 9

6 Improvements Improved haplotype-aware assembly. Improved handling of insertions and deletions with small overlap of alignments. Improved refinement runtime by converting from double precision to single precision floats. Improved haplotype refinement runtime by keeping track of regions of a given genome map that has converged and skipping those regions. Improved sensitivity and positive predictive value of calling heterozygous insertions and deletions, especially above 100 kbp. Improved sensitivity and positive predictive value of calling translocation breakpoints. Bionano Solve Pipeline Added bash script to TAR and GZIP file results for Bionano Access import function (and a command line argument to disable it). Added simplified assembly summary report. Added Irys- and Saphyr-specific cluster arguments XML files. Added a feature to support memory arguments in cluster arguments. Arguments supplied in the cluster arguments XML files would automatically override those in the assembly parameters XML files. Added BED files for hg38 reference genome. Added enzyme-specific versions (BspQI and BssSI). Improved logging in pipeline report and cluster logs. Moved default assembly parameters XML files to RefAligner. Updated BED files for hg19 reference genome. Added enzyme-specific versions (BspQI and BssSI). The assembly pipeline -H option now takes an argument to load the hg19 reference genome or hg38 reference genome BspQI-specific BED file. Updated job merging arguments. Updated handling of the -minlen parameter for bnx_sort to accommodate for cases where stretch is significantly different from normal. Final -minlen is applied to either in autonoise1 or in bnx_split if autonoise is disabled. SVMerge Added new SVMerge algorithm to merge SV output from two single-enzyme assemblies. SVMerge currently supports merging of insertion, deletion, and translocation breakpoint calls. SVMerge provides SV calling sensitivity and specificity. For more details, see Bionano Solve Theory of Operation: Structural Variant Calling (part number 30110) Rev B, Bionano Solve v3.0.1 Release Notes Page 6 of 9

7 Hybrid Scaffold One-enzyme Hybrid Scaffold Added compressed output for import and export file purposes. Updated output summary report. Two-enzyme Hybrid Scaffold Added new two-enzyme Hybrid Scaffold workflow for integration of two single-enzyme assemblies with a sequence assembly. Moved the map editing features to Bionano Access. Although users can manually manipulate cuts in the cut file when interacting at the command line, Bionano Access supports a graphical interface for map editing. The AGP and FASTA files output from the Hybrid Scaffold pipeline passed validation based on a tool NCBI provided. SMAP-to-VCF Converter Added support for converting translocation breakpoints (in addition to insertion and deletion calls). Added specific tags for compliance with dbvar. For example, experiment ID. Updated output for compliance with standard VCF v4.2 specifications. Updated input parameters: The SV detection XMAP file output path is now required. New optional parameters, including: Sample type to include human Reference accession Sample name Experiment ID A separate SVMerge-to-VCF converter is available at Github for conversion of SVMerge results to VCF v4.2 format. Variant Annotation Pipeline (beta version) Added new automated variant annotation pipeline to streamline family trio analysis. Structural variants in the proband are compared against a Bionano internal control sample database. Inheritance status of the proband's structural variants is established by comparing to the parents' calls. The parents' original molecules are examined to determine if the proband's structural variants are present at low allele frequencies in the parents. Variants are compared to a control database of phenotypically normal samples. Added a similar workflow for case-control analysis Rev B, Bionano Solve v3.0.1 Release Notes Page 7 of 9

8 Known Issues and Limitations Adaptive memory usage algorithm could be activated during assembly under different server environments. As a result, there could be slight differences in the SV output. Users with non-standard cluster or server configurations may experience suboptimal runtime performance. Clusters not running SGE scheduling will continue to require manual starting of the pipeline via command-line and importing of the results into Bionano Access. Insertion and deletion calls of less than 500 bp are included in the SMAP output; however, calling of such small events has not been extensively validated, and so they are assigned confidence of -1. It is recommended that a confidence threshold larger than or equal to 0 be applied in the SV table drop-down menu in order to filter out SV entries with confidence of -1 if the user is only interested in validated SV types. By imposing a confidence threshold, other SV types that have not been validated such as inversion breakpoints (whose confidence is currently also assigned as -1) would be filtered out as well. In the summary for the two-enzyme hybrid scaffold results, we report the numbers of NGS contigs and the total length of NGS contigs that only align to the remaining single-enzyme hybrid scaffolds (i.e. scaffolds that cannot be merged into two-enzyme hybrid scaffolds). See highlighted text below in red from hybrid_scaffold_informatics_report.txt: Those numbers can sometimes be zeroes as a result of a known defect. This defect is only a reporting issue and does not affect the scaffold results nor the assessment of scaffold accuracy. This defect will be addressed in the next release Rev B, Bionano Solve v3.0.1 Release Notes Page 8 of 9

9 Technical Assistance For technical assistance, contact Bionano Genomics Technical Support. You can retrieve documentation on Bionano products, SDS's, certificates of analysis, frequently asked questions, and other related documents from the Support page or by request through and telephone. Type Contact Phone Hours of Operation: Monday through Friday, 9:00 a.m. to 5:00 p.m., PST US: +1 (858) Website Rev B, Bionano Solve v3.0.1 Release Notes Page 9 of 9