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8-2- 11 Meeting

8-2- 11 Meeting. Ember Genome Assembly Update. Assembly Galaxy TREAT Pratik Others?. E. coli – Wallclock / %CPU. S. pombe – Wallclock / %CPU. hg18 chr10 – Wallclock / %CPU. E. coli – Memory Usage. S. pombe – Memory Usage. hg18 chr10 – Memory Usage. Trial 1 – v. 1.1.04.

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8-2- 11 Meeting

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  1. 8-2-11 Meeting

  2. Ember Genome Assembly Update • Assembly • Galaxy • TREAT • Pratik • Others?

  3. E. coli – Wallclock / %CPU

  4. S. pombe– Wallclock / %CPU

  5. hg18 chr10 – Wallclock / %CPU

  6. E. coli – Memory Usage

  7. S. pombe – Memory Usage

  8. hg18 chr10 – Memory Usage

  9. Trial 1 – v. 1.1.04

  10. Trial 1 – v. 1.1.04

  11. Trial 2 – v. 1.1.05 (latest)

  12. Next… • Yoruba genome • Downloading from NCBI SRA (since last Thurs) • IMO: Aspera is terrible • ABYSS is now working, do we want to repeat some of these? • PE-asm and SOAPdenovo also present

  13. More on Ember • Jian Ma, Sheng Zhong, Matt Hudson all have accounts on Ember • What do we want from them? • Matt’s group: still awaiting results from Kranthi on SOAPdenovo (was supposed to get them last night) • Sheng’s group is running jobs now • Jaebum (Jian’s postdoc) has just started

  14. Other topics • Galaxy • Local jobs seem to work (pulled data from UCSC, uploaded seqs and aligned with ClustalW) • EMBOSS, Bowtie, bwa, samtoolsalso installed, need testing • Deployment plan… • Luigi?

  15. TREAT • Awaiting feedback from Asif re: bad *.tar.gz file • Proceeding anyway with what we have • Gloria?

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