Nextera Long Mate Pair analysis and processing tool
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README.md

NextClip

Nextera Long Mate Pair analysis and processing tool. See manual for installation and instructions.

The 'examples' directory contains example reports and a partial set of reads for a (relatively low quality) Nextera library. See the ReadMe file inside the examples directory for details of running the examples.

To hear about updates to NextClip, please follow @richardmleggett on Twitter: https://twitter.com/richardmleggett

Changes in v1.3

Bug fixes

  • Improved ability to spot junction adaptor due to bug in previous logic.
  • Removed some crashes that can occur if some of the stats counts are zero (ie. dividing zero by number of reads creates error).
  • Corrected LSF submission to request correct amount of memory for NextClip (and provided option which will report memory requirements before running NextClip).
  • The min_length parameter was 1 base out (i.e. specifying 25 gave reads of 24) - this is fixed, meaning that yields will appear to go down slightly. You can always decrease min_length to 24 if you want to recover this.
  • Fixed PCR duplicate stats being wrong for counts > 99.
  • Fixed help wording.

Improvements

  • NextClip outputs number of bases written for each category and the pipeline PDF report shows this as well as approximate genome coverage.
  • Ability to pass parameters through to the pipeline (e.g. minimum width, trim ends etc.).
  • You can specify the pipeline stage to start at, so no need to redo all analysis in the event of a fail.
  • The scripts directory is found automatically - no need to set it during installation.
  • Moved PCR duplicate kmer offset to avoid lower quality bases at start of read. Should provide slightly more accurate estimates of PCR duplication.
  • Queue name can be specified when running with LSF.
  • Reduced size of hash table used to store PCR duplicates.