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