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Sep 23rd, 2014
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  1. This isn't Samarth's assembly, but a test run I did on the side.
  2. It's a different assembly than the one he presented at GI2014, I naively inputted his HGAP-corrected reads and ran with:
  3.  
  4. fastqToCA -technology pacbio-corrected -libraryname $libname -reads $input > ca_assembly.frg
  5. runCA ca_assembly.frg -p $libname -d `pwd`/tmp
  6.  
  7. I recall that samarth did some post-filtering on the assembly and maybe other pre-filtering. Mine is way bigger (159 Mbp instead of expected 50 Mbp), and smaller NG50 (15 kbp).
  8.  
  9. [rxc48@brubeck celera_corrected_5kbp_filtered]$ cat ca_assembly.gkpStore.info
  10. libIID bgnIID endIID active deleted mated totLen clrLen libName
  11. 0 1 636424 636424 0 0 2338694435 2338694435 GLOBAL
  12. 0 0 0 0 0 0 0 0 LegacyUnmatedReads
  13. 1 1 636424 636424 0 0 2338694435 2338694435 ca_assembly
  14.  
  15.  
  16. [rxc48@brubeck celera_corrected_5kbp_filtered]$ cat ca_assembly.gkpStore.err
  17.  
  18. Starting file '/scratch/rayan/ca_assembly.frg'.
  19.  
  20. Processing SINGLE-ENDED SANGER QV encoding reads from:
  21. '/scratch/rayan/data/corrected_5kbp_filtered_female.fastq'
  22.  
  23.  
  24. GKP finished with no alerts or errors.
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