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SMRT Analysis Release Notes v2.0

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fripp edited this page Apr 16, 2013 · 27 revisions
  • [Introduction] (#Intro)
  • [Installation] (#Install)
  • [New Features in v2.0] (#New)
  • [Fixed Issues in v2.0] (#Fixed)
  • [Known Issues in v2.0] (#Known)

Introduction

SMRT Analysis software performs automated and distributed secondary analysis of sequencing data generated by the PacBio® System.

Installation

For installation instructions, see SMRT® Analysis Software Installation.

New Features in v2.0

###SMRT® Portal###

  • Now includes the RS_HGAP_Assembly protocol to perform pre-assembly, assembly with Celera Assembler, and assembly polishing with Quiver, all in one integrated workflow.
  • RS_Modification_and_Motif_Analysis and RS_Modification_Detection protocols now include improved accuracy for XL-C2 chemistry. Base modification detection with C2 continues to be supported as well.
  • RS_Modification_and_Motif_Analysis now supports analysis of fractionally methylated or modified base positions within a sample.
  • You can now upload references using SMRT Portal without first placing the reference FASTA file in the dropbox by using the Select Reference Sequence Files(s) to Import dialog.
  • The Motif report now includes separate histograms of modification QV per motif.
  • Now displays simplified metric names, including Polymerase Read metrics and Read Length of Insert. To shorten the names, the report tooltip definitions now clarify whether a particular metric refers to the mean or another summary statistic. Several detailed metrics are no longer displayed on the Summary page; they continue to be displayed in the more detailed reports.
  • The View Log window now includes a link to download the log file.
  • A new web service call, the Cleanup Function, cleans up duplicate SMRT Cells located at different paths, if the cells are unassociated with jobs. When you scan and import SMRT Cells from SMRT Portal and the same SMRT Cell ID already exists, the existing path is updated to the new location. No duplicate entries are created.

###SMRT® View###

  • Multiple UI enhancements:
  • When run in stand-alone mode, uses the native file system browser.
  • The toolbar includes new, more intuitive icons for base modifications and showing/hiding bases.
  • You can now remove tracks from the display without exiting SMRT View.
  • Now displays variant call tracks per barcode.

###SMRT® Pipe###

  • Many SMRT Pipe command-line tools now include improved documentation and command-line examples.
  • Now includes a new examples directory.
  • Quiver was enhanced to reduce errors in long dinucleotide repeats.

###Installation###

  • The installation now checks for version mismatches on compute nodes.
  • Includes many small improvements to the upgrade and post-installation scripts.
  • The /opt/smrtanalysis/doc/ directory in the SMRT Analysis installation now includes a README file pointing to the online documentation.
  • The SMRT Analysis installation documentation is now delivered as a web page: SMRT® Analysis Software Installation.

Fixed Issues in v2.0

###SMRT® Pipe##

  • The minor and compound variant detection algorithm now allows adjustment of the minimum coverage requirement. (21474)
  • The long insert control was renamed from Strobe_v1 to 4kb_Control_c2, and is intended for use only with C2 sequencing runs. The shorter insert control is now called 600bp_Control_c2. (19483)
  • bash5tools.py now outputs subreads within the HQ region only. (21565)
  • To more accurately show the uniformity of coverage in BLASR mapping, the default is now to place repeats randomly. (21769)
  • Mapping results are now reproducible due to fully deterministic pseudo-randomization. (22126)
  • GMAP download link names were changed for consistency and intuitiveness. (22238)
  • The consensus sequence no longer includes N's by default when there is no evidence. Instead, the reference base is output, but in lowercase. (22227)
  • Now correctly produces a Barcoded Reads FASTQ file for barcode output. (22341)

###SMRT® Pipe - Assembly###

  • The Pre-Assembler protocol now outputs summary metrics for the pre-assembly. (22631)
  • The P_PreAssembler protocol now correctly writes thetmp.fasta and tmp.fastq files to the correct sharedTmp directory. (22964)
  • The P_PreAssembler protocol now completes correctly when using SMRT Cell inputs created by different ICS versions. (22205)

###SMRT® Pipe - Reference Uploader###

  • The reference import mechanism now rejects duplicate FASTA sequences. (21947)

###Installation/Upgrades###

  • The conf_main.log file was moved to common/log/install. (22612)
  • The conf_main.log file now contains all output from the installation. (22200)
  • The upgrade_and_configure script now manages soft links and Tomcat and Kodos services. (22599)
  • The upgrade_and_configure script now displays a warning if reference repository updates are required, as this operation may take a long time. (22324)
  • The CentOS 5.6 binaries for SMRT Analysis now include libgfortran.so.3. (22464)

###SMRT® Analysis System###

  • The sample data sets were updated. (22839)
  • The cmp.h5 file was updated to address barcoding and multi-streamed base files. (22491).

Known Issues in v2.0

###SMRT® Portal###

  • In the Create New and View Data pages, Advanced search may not display the calendar on some browsers. (17275)
  • Exporting Table Data does not correctly export Group names. (22567)
  • Exporting Table data from the Create New Job page results in an empty version field. (22627)
  • In the View Data page, sorting by Groups returns empty values. (22666)
  • In the SMRT Cell Available table, sorting on Version returns empty values. You also cannot search the table on Version. (22687)
  • You cannot select an inactive protocol in the Manage Secondary Analysis Protocols page. (22068)
  • You cannot add SMRT Cells after saving a job containing no cells. (22400)

###SMRT® Pipe - Mapping###

  • BLASR does not process renamed files correctly. (21439)
  • BLASR may align subreads from the same ZMW to different genomic coordinates. (20755)

###SMRT® Pipe - System###

  • MySQL passwords containing & (ampersand) characters are not handled correctly. (22761)
  • The configure_smrtanalysis.sh script aborts when [y/n] is not chosen. (22323)
  • CCS allpass mode produces incorrect results when --placeRepeatsRandomly is specified. (22935)
  • BaseQV is not passed to the SAM file in the P_GMAP module. (21884)

For Research Use Only. Not for use in diagnostic procedures. © Copyright 2010 - 2013, Pacific Biosciences of California, Inc. All rights reserved. Information in this document is subject to change without notice. Pacific Biosciences assumes no responsibility for any errors or omissions in this document. Certain notices, terms, conditions and/or use restrictions may pertain to your use of Pacific Biosciences products and/or third party products. Please refer to the applicable Pacific Biosciences Terms and Conditions of Sale and to the applicable license terms at http://www.pacificbiosciences.com/licenses.html.

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