Binan Slve v3.2.1 Release Ntes Dcument Number: 30221 Dcument Revisin: A Fr Research Use Only. Nt fr use in diagnstic prcedures. Cpyright 2018 Binan Genmics, Inc. All Rights Reserved.
Legal Ntice Fr Research Use Only. Nt fr use in diagnstic prcedures. This material is prtected by United States Cpyright Law and Internatinal Treaties. Unauthrized use f this material is prhibited. N part f the publicatin may be cpied, reprduced, distributed, translated, reverse-engineered r transmitted in any frm r by any media, r by any means, whether nw knwn r unknwn, withut the express prir permissin in writing frm Binan Genmics. Cpying, under the law, includes translating int anther language r frmat. The technical data cntained herein is intended fr ultimate destinatins permitted by U.S. law. Diversin cntrary t U. S. law prhibited. This publicatin represents the latest infrmatin available at the time f release. Due t cntinuus effrts t imprve the prduct, technical changes may ccur that are nt reflected in this dcument. Binan Genmics reserves the right t make changes in specificatins and ther infrmatin cntained in this publicatin at any time and withut prir ntice. Please cntact Binan Genmics Custmer Supprt fr the latest infrmatin. 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 Prducts f Binan Genmics may be cvered by ne r mre U.S. r freign patents. Trademarks The Binan Genmics lg and names f Binan Genmics prducts r services are registered trademarks r trademarks wned by Binan Genmics in the United States and certain ther cuntries. Binan Genmics, Irys, IrysView, IrysChip, IrysPrep, IrysSlve, Saphyr, Saphyr Chip, and Binan Access are trademarks f Binan Genmics, Inc. All ther trademarks are the sle prperty f their respective wners. N license t use any trademarks f Binan Genmics is given r implied. Users are nt permitted t use these trademarks withut the prir written cnsent f Binan Genmics. The use f these trademarks r any ther materials, except as permitted herein, is expressly prhibited and may be in vilatin f federal r ther applicable laws. Cpyright 2018 Binan Genmics, Inc. All rights reserved. Page 2 f 7 30221 Rev A, Binan Slve v3.2.1 Release Ntes
Table f Cntents Legal Ntice... 2 Intrductin... 4 References... 4 RefAligner... 4 Binan Slve Pipeline... 4 Hybrid Scaffld... 5 Variant Anntatin Pipeline... 5 SVMerge... 5 VCF Cnverter... 5 Other Knwn Issues and Limitatins... 5 Technical Assistance... 7 30221 Rev A, Binan Slve v3.2.1 Release Ntes Page 3 f 7
Intrductin This dcument describes the release f Binan Slve v3.2.1. We prvide an verview f the fixes and imprvements as they impact RefAligner, the Binan Slve Cmpute pipeline, the Hybrid Scaffld pipeline, the Variant Anntatin Pipeline, SVMerge, and the VCF cnverter. These tls have been ptimized t wrk with the new Direct Label and Stain (DLS) chemistry. References Visit https://binangenmics.cm/supprt-page/binan-slve/ fr file frmat specificatins and Thery f Operatin dcuments. RefAligner New XML files with ptimized parameters are prvided fr analyzing DLS data. Imprved handling f large nn-unique genmic regins (fr example, regins assciated with segmental duplicatins), which culd create ambiguity in the assembly. We call these cmplex multipath regins (CMPRs). Map labels within these regins are flagged in a de nv fashin during assembly, and the map is cut. We als prvide the ptin t nly flag the relevant labels but nt cut the maps; in that case, we recmmend manual inspectin in Binan Access and careful interpretatin f the resulting assembly N50. Imprved verall runtime perfrmance and handling f utlier cases. See Thery f Operatin dcuments fr Structural Variant calling (PN# 30110) and Hybrid Scaffld (PN# 30073) fr latest runtime metrics. Imprved sensitivity f detecting insertins and deletins between 500 bp and 1 kbp especially when used with DLS. Imprved sensitivity f detecting translcatins between 50 kbp and 100 kbp when used with DLS. Imprved sensitivity f detecting duplicatins and inversins between 30 kbp and 100 kbp when used with DLS. Binan Slve Pipeline Implemented a new cpy number algrithm, whse results can be visualized in Binan Access. It supprts integrated (run by default as part f assembly) and standalne usages. It prvides better sensitivity and PPV fr events > 500 kbp. Pre-prcessed cntrl data t supprt hg19/38 and BspQI/BssSI/DLE-1 are prvided. Wrapper scripts fr pre-prcessing custm cntrl data (fr example, nn-human datasets) are prvided. See Intrductin t Cpy Number Analysis fr detail (PN# 30210). Nte: Perfrmance data were based n calling the crrect regins where cpy number changes ccurred. Althugh whether cpy number increased r decreased is accurate, the exact cpy number state (fr example, 3 cpies vs. 4 cpies) may nt be as accurate. Updated BED files fr anntating insertin, deletin, and translcatin breakpint calls. Updated summary reprt fr easier interpretatin. Page 4 f 7 30221 Rev A, Binan Slve v3.2.1 Release Ntes
Hybrid Scaffld Optimized with ne-enzyme and tw-enzyme pipeline t handle DLS data. Imprved anchring f sequence cntigs using a new 2-stage alignment apprach that maximizes sensitivity and runtime perfrmance. Users culd further fine-tune the stringency by adjusting the alignment p-value threshld in Binan Access. Imprved handling f cmplex multi-path regins (CMPRs) t prevent frmatin f chimeric scafflds. Imprved verall runtime by ptimizing multiple cmpnents in the pipeline. Updated utput summary reprts. Added.gap file utput t ne-enzyme Hybrid Scaffld cmpressed package. Nte 1: Scafflding DLS assemblies with Hi-C assemblies, which typically cntain significant rder and rientatin errrs, is nt recmmended. If attempted, users are recmmended t manually curate and reslve cnflicts between the Binan maps and Hi-C scafflds. Nte 2: Three-enzyme Hybrid Scaffld may be pssible but has nt been validated. Variant Anntatin Pipeline Added anntatin f duplicatin calls. Added new DLE-1 cntrl data fr estimating variant frequencies. Added enzyme-specific variant frequency estimates. SVMerge SVMerge f single-enzyme variant anntatin utput nw includes enzyme-specific frequency estimates. We utput the maximum f the enzyme-specific frequency estimates. Nte: With the launch f the DLS chemistry and the labeling enzyme DLE-1, the need t cnduct tw experiments with tw enzymes (SVMerge wrkflw) in rder t fully cver the genme and achieve the highest sensitivity fr structural variant detectin is bviated. Fr whle genme SV discvery, we nw recmmend a single-enzyme wrkflw with DLS. Thus, SVMerge with DLS data is nt recmmended. SVMerge with data frm tw nickases is still supprted and may be utilized fr specialized applicatins. VCF Cnverter Updated gentype utput: 0/1 is utput fr heterzygus calls, 1/1 fr hmzygus calls, and./. fr unknwn calls. Other Knwn Issues and Limitatins Adaptive memry usage algrithm culd be activated during assembly under different server envirnments. As a result, there culd be slight differences in the SV utput. Users with nn-standard cluster r server cnfiguratins may experience subptimal runtime perfrmance. Hybrid Scaffld utput FASTA/AGP files may cntain header lines with whitespaces and wuld nt 30221 Rev A, Binan Slve v3.2.1 Release Ntes Page 5 f 7
pass NCBI AGP validatin. Hapltype-aware refinement n nn-human datasets is nt a supprted feature, and its use may have unintended cnsequences. Large heterzygus duplicatins may be called as hmzygus when the allele with a single cpy is nt successfully assembled, if t few mlecules span acrss the entire duplicatin regin. Page 6 f 7 30221 Rev A, Binan Slve v3.2.1 Release Ntes
Technical Assistance Fr technical assistance, cntact Binan Genmics Technical Supprt. Yu can retrieve dcumentatin n Binan prducts, SDS's, certificates f analysis, frequently asked questins, and ther related dcuments frm the Supprt website r by request thrugh e-mail and telephne. Type Email Cntact supprt@binangenmics.cm Phne Hurs f Operatin: Mnday thrugh Friday, 9:00 a.m. t 5:00 p.m., PST US: +1 (858) 888-7600 Website www.binanngenmics.cm/supprt 30221 Rev A, Binan Slve v3.2.1 Release Ntes Page 7 f 7