Francisella tularensis novicida GA99-3548: Difference between revisions
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Center: Broad | Center: Broad | ||
Status: Assembly (18 contigs) | Status: Assembly (18 contigs) | ||
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[[Media:NC_008601-NZ_ABAH00000000.png|NC_008601-NZ_ABAH00000000.png]] | [[Media:NC_008601-NZ_ABAH00000000.png|NC_008601-NZ_ABAH00000000.png]] | ||
Mummerplot Francisella tularensis noviciada U112 (complete genome) vs Francisella tularensis novicida GA99-3548 | Mummerplot Francisella tularensis noviciada U112 (complete genome) vs Francisella tularensis novicida GA99-3548 | ||
No rearrangements can be noticed | No rearrangements can be noticed; several indels (up to 24KB) | ||
== Assembly == | == Assembly == | ||
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=> 11 scaff, 24 contigs, 1,830,675 bp | => 11 scaff, 24 contigs, 1,830,675 bp | ||
'''2007_0816_WGA''' | '''2007_0816_WGA -> best''' | ||
Only WGS reads | Only WGS reads | ||
runCA-OBT.pl => new read clr, new library insert estimates | runCA-OBT.pl => new read clr, new library insert estimates | ||
| Line 66: | Line 66: | ||
use read clr from 2007_0807_WGA | use read clr from 2007_0807_WGA | ||
=> 13 scaff, 23 contigs, 1,832,735 bp | => 13 scaff, 23 contigs, 1,832,735 bp | ||
autoJoiner was run on this assembly ; reference ID's had to be "truncated" ([^|.]); no gaps were filled | |||
'''2007_0820_AMOScmp-OBT-454''' | |||
use read clr from 2007_0807_WGA + 454 reads | |||
=> 13 scaff, 35 contigs, 1,839,125 bp | |||
Latest revision as of 17:55, 22 August 2007
Center: Broad Status: Assembly (18 contigs)
Data
Reference:
Name Length %GC NZ_ABAH01000001.1 77907 33.26 NZ_ABAH01000002.1 3200 35.62 NZ_ABAH01000003.1 143439 32.80 NZ_ABAH01000004.1 4000 35.33 NZ_ABAH01000005.1 55000 33.33 NZ_ABAH01000006.1 336 46.73 high GC% NZ_ABAH01000007.1 560 34.29 NZ_ABAH01000008.1 623050 31.76 NZ_ABAH01000009.1 18017 32.28 NZ_ABAH01000010.1 238333 32.07 NZ_ABAH01000011.1 312 44.23 high GC% NZ_ABAH01000012.1 466 44.21 high GC% NZ_ABAH01000013.1 293238 32.05 NZ_ABAH01000014.1 171625 34.06 NZ_ABAH01000015.1 1155 48.14 high GC% NZ_ABAH01000016.1 344 46.80 high GC% NZ_ABAH01000017.1 301 46.18 high GC% NZ_ABAH01000018.1 214208 32.15 Total 1,845,491 bp 1,910,031 bp in U112(complete) => 64,540 bp in gaps
Traces: from NCBI TA
Libraries:
CENTER PROJECT STRAIN LIB TYPE SIZE STDEV COUNT Location WIBR G909 GA99-3548 G909A2 WGS 4,500 450 768 TA WIBR G909 GA99-3548 G909A4 WGS 4,500 450 768 TA WIBR G909 GA99-3548 G909A3 WGS 4,500 450 23,040 TA WIBR G921 GA99-3548 454-414 454 . . 17,731 TA Total 42,307
NC_008601-NZ_ABAH00000000.png Mummerplot Francisella tularensis noviciada U112 (complete genome) vs Francisella tularensis novicida GA99-3548 No rearrangements can be noticed; several indels (up to 24KB)
Assembly
Locations
/fs/szasmg2/Bacteria/F_tularensis_novicida_GA99-3548
2007_0816_AMOScmp
Uses default trimming => 11 scaff, 24 contigs, 1,830,675 bp
2007_0816_WGA -> best
Only WGS reads runCA-OBT.pl => new read clr, new library insert estimates
clr got shorter by runing OBT (usually is the opposite) . #traces min median max sum mean stdev n50 CLIPPING 23721 0 857 1034 20118102 848.11 77.58 859 OBT 22543 65 783 917 17315299 768.1 76.93 786
lib: G909A3 mean=5996.958 stdev=144.620 (larger insert than original value) => 8 scaff, 18 contigs, 1,839,522 bp
2007_0816_AMOScmp-OBT
use read clr from 2007_0807_WGA => 13 scaff, 23 contigs, 1,832,735 bp autoJoiner was run on this assembly ; reference ID's had to be "truncated" ([^|.]); no gaps were filled
2007_0820_AMOScmp-OBT-454
use read clr from 2007_0807_WGA + 454 reads => 13 scaff, 35 contigs, 1,839,125 bp