Francisella tularensis tularensis ATCC6223: Difference between revisions
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Center: Baylor | Center: Baylor | ||
Status: Assembly (88 contigs) | Status: Assembly (88 contigs; 1,757,628 bp; maxLen=133,694 bp; avgLen=19,973 bp) | ||
== Data == | == Data == | ||
'''Libraries:''' | '''Libraries:''' | ||
CENTER PROJECT STRAIN | CENTER PROJECT STRAIN LIB TYPE SIZE STDEV COUNT LOCATION | ||
BCM BFTF ATCC6223 BFTFP WGS 6,250 1,250 2,144 TA | BCM BFTF ATCC6223 BFTFP WGS 6,250 1,250 2,144 TA | ||
BCM 4WG_FTUL.AT ATCC6223 4WG_FTUL.AT_000SA 454 . . 408,780 TA | BCM 4WG_FTUL.AT ATCC6223 4WG_FTUL.AT_000SA 454 . . 408,780 TA | ||
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/fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/ | /fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/ | ||
''' | '''2007_0821_AMOScmp-454 -> best''' | ||
=> 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp | |||
272,522 singletons ; all 454 paired reads are left as singletons | |||
'''2007_0821_AMOScmp-454-SchuS4''' | |||
uses Schu S4 (complete) as reference | |||
=> 1 scaff, 194 contigs, 1,759,427 bp | |||
=> 2 large areas with coverage twice as deep as average | |||
=> 3 large areas with no 454 coverage | |||
'''2007_0821_AMOScmp-454-FSC198''' | |||
uses FSC198 (complete) as reference | |||
=> 1 scaff, 195 contigs, 1,761,838 bp | |||
=> 2 large areas with coverage twice as deep as average | |||
=> 3 large areas with no 454 coverage | |||
'''2007_0821_AMOScmp-454-WY96-3418''' | |||
uses WY96-3418(complete) as reference | |||
=> 1 scaff, 144 contigs, 1,761,838 bp | |||
=> 2 large areas with coverage twice as deep as average | |||
=> 4-5 large areas with no 454 coverage | |||
'''Problem''' | |||
lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; could not run newbler on both 454 libraries | |||
Latest revision as of 20:23, 23 August 2007
Center: Baylor Status: Assembly (88 contigs; 1,757,628 bp; maxLen=133,694 bp; avgLen=19,973 bp)
Data
Libraries:
CENTER PROJECT STRAIN LIB TYPE SIZE STDEV COUNT LOCATION BCM BFTF ATCC6223 BFTFP WGS 6,250 1,250 2,144 TA BCM 4WG_FTUL.AT ATCC6223 4WG_FTUL.AT_000SA 454 . . 408,780 TA BCM 4WG_FTUL.AT ATCC6223 4WG_FTUL.AT_000pA 454 . . 218,232 SRA ? Total 629,156
Assembly
Locations:
/fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/
2007_0821_AMOScmp-454 -> best
=> 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp 272,522 singletons ; all 454 paired reads are left as singletons
2007_0821_AMOScmp-454-SchuS4
uses Schu S4 (complete) as reference => 1 scaff, 194 contigs, 1,759,427 bp => 2 large areas with coverage twice as deep as average => 3 large areas with no 454 coverage
2007_0821_AMOScmp-454-FSC198
uses FSC198 (complete) as reference => 1 scaff, 195 contigs, 1,761,838 bp => 2 large areas with coverage twice as deep as average => 3 large areas with no 454 coverage
2007_0821_AMOScmp-454-WY96-3418
uses WY96-3418(complete) as reference => 1 scaff, 144 contigs, 1,761,838 bp => 2 large areas with coverage twice as deep as average => 4-5 large areas with no 454 coverage
Problem
lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; could not run newbler on both 454 libraries