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Pacific Biosciences of California, Inc. Message Board

  • paulieme60 paulieme60 Aug 8, 2013 3:15 PM Flag

    LSC is a long read error correction tool.

    It offers fast correction with high sensitivity
    and good accuracy.
    Latest News: LSC 0.3 -- Support BWA, Bowtie2, RazerS3, much faster and more accurate ... read more
    .Getting Started
    These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.
    •Read the LSC_requirements for running LSC.
    •Download and set-up the LSC package
    •Follow the tutorial to see how LSC works on some example data.
    •Check the manual if anything is unclear.
    •You're ready, Happy LSCing!
    Latest publication
    Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong
    Improving PacBio Long Read Accuracy by Short Read Alignment [preprint]
    PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679
    Latest News
    08-07-2013: Big changes in LSC 0.3
    In LSC 0.3, we have a few updates. They are very IMPORTANT updates, new features and small fixes
    Very IMPORTANT updates:
    •Support for Bowtie2 and RazerS3 as initial aligners. Now, BWA, Bowtie2, RazerS3 and Novoalign work in LSC. Please see the comparison details of aligners in the "Short read - Long read aligner#manual".
    •Added SR length coverage percentage on LR (SR-covered length/full length of corrected LR) to corrected_LR output file. Here is an example, where the last number 0.82 is the SR length coverage percentage on LR:
    m111006_202713_42141_c100202382555500000315044810141104_s1_p0/18941/365_1361|0.82
    •Added support for three modes for step-wise runs:
    mode 0: end-to-end
    mode 1: generating LR_SR.map file
    mode 2: correction step
    •Generating FASTQ output format based on correction probability given short read coverage. Please refer to LSC paper and manual page for more details. You can select well-corrected reads for downstream analyses by using the quality in FASTQ output or SR length coverage percentage above. Please the the filtering in the "Output#manual". (part 1 of 2)

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    • (part 2 of 2) Output#manual". New features

      •Used the python path in the cfg file instead of default user/bin path
      •Added option (-clean_up) to remove intermediate files or not (Note: important/useful ones will still be there in temp folder)
      •Support for input fastq format for LR (long reads) and/or SR (short reads)
      •Updated default BWA and novoalign commands options
      •Printing out original LR names in the output file
      •Support for printing out version number using -v/-version option
      Small bug fixed

      •Fixed in removing XZ pattern printed out at the end of some uncorrected_LR sequences
      •Fixed samParser bug (which was ignoring some valid alignments in BWA output)

 
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