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PHASIS (v3) - PHAS Inspection Suite

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@atulkakrana atulkakrana released this 05 Apr 01:09
· 7 commits to master since this release
v3.3
e054d7c

Note: PHASworks/PHASter is now PHASIS

See wiki for more information on installation, usage and description of results.

Enhancements:

phasdetect (previously named as phaser):

  • Added a new index integrity checker to accommodate different index formats from the Bowtie and to ensure the completeness of genome index
  • Improved core assignment, critical improvement for machines with eight cores or less
  • Fixed a regression affecting analyses for large genomes using index with 64-bit numbers [25-Apr-2015]

phasmerge (previously named as collapser):

  • Added the annotation function, which enables matching of PHAS loci to genome annotations; and can be used to identify PHAS transcripts when supplied with GTF file for transcriptome assembly by mapping it to genome
  • Added the compare mode, which allows comparison between two different PHAS summaries
  • Updated the runType modes for better speed optimization
  • Improved a couple of functions to maximize parallelization - significant speed gain over previous version

phastrigs (previously named as revFerno):

  • Added a new ‘search space’ setting to define search space for triggers - it takes values in PHAS cycles i.e. value of 3 will scan for trigger site three phased positions to left and three to right of P1
  • Minor bugfixes

And,

  • complete dependency checks before running tool(s)
  • better error handing

Report issues here
Check wiki here
Track progress on bug fixes and new features here

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