<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41148?offset=120 https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment Thu, 06 Sep 2018 16:27:35 -0500 https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment <![CDATA[LSC: Improving PacBio Long Read Accuracy by Short Read Alignment]]>
  • Added Command line argument support.
  • Multi-stage execution modes.
  • Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N.
  • Better compressed intermediate files.
  • Added utilities folder.
  • Added support for multiple short read files.
  • Removed use of configuration file.

    • Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/bookmarks/view/39640/flas-fast-and-high-throughput-algorithm-for-pacbio-long-read-self-correction Sat, 22 Jun 2019 12:16:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39640/flas-fast-and-high-throughput-algorithm-for-pacbio-long-read-self-correction <![CDATA[FLAS: fast and high throughput algorithm for PacBio long read self-correction.]]> FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy.

    Address of the bookmark: https://github.com/baoe/flas

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools Wed, 15 Mar 2017 14:19:01 -0500 https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools <![CDATA[Pacbio Long Reads Compatible Software and Tools]]> The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A separate page lists commercial software.

    Know of any other open source software for PacBio data? Email us.

    Software categories:

    Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

    ]]>     Archana Malhotra     https://bioinformaticsonline.com/bookmarks/view/36867/cerulean-a-hybrid-assembly-using-high-throughput-short-and-long-reads Tue, 05 Jun 2018 10:10:15 -0500 https://bioinformaticsonline.com/bookmarks/view/36867/cerulean-a-hybrid-assembly-using-high-throughput-short-and-long-reads <![CDATA[Cerulean: A hybrid assembly using high throughput short and long reads]]> Address of the bookmark: https://sourceforge.net/projects/ceruleanassembler/

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/blog/view/38277/understating-pacbio-reads-name Fri, 23 Nov 2018 07:36:46 -0600 https://bioinformaticsonline.com/blog/view/38277/understating-pacbio-reads-name <![CDATA[Understating pacbio reads name !]]> m140415_143853_42175_c100635972550000001823121909121417_s1_p0/553/3100_11230 0.99 24 └1┘└─────2─────┘└──3─┘└────────────────4────────────────┘└5┘└6┘└7┘└────8────┘└─9─┘└10┘
    1. "m" = movie
    2. Time of Run Start (yymmdd_hhmmss)
    3. Instrument Serial Number
    4. SMRT Cell Barcode
    5. Set Number (a.k.a. "Look Number". Deprecated field, used in earlier version of RS)
    6. Part Number (usually "p0", "X0" when using expired reagents)
    7. ZMW hole number
    8. Subread Region (start_stop using polymerase read coordinates)
    9. readScore
    10. barcodeScore
    ]]>     BioJoker