Genome assembly3
From CSBLwiki
(Difference between revisions)
| (13 intermediate revisions not shown) | |||
| Line 1: | Line 1: | ||
<i>Verrucosispora</i> sp. | <i>Verrucosispora</i> sp. | ||
| + | =Circular view= | ||
| + | [[File:NC 015434.png|450px]] | ||
| + | [[File:NC 015409.png|250px]] | ||
=Log= | =Log= | ||
#Illuminia PE -> ABySS -> Fake reads | #Illuminia PE -> ABySS -> Fake reads | ||
| Line 5: | Line 8: | ||
#Fake read + 454(2007.06,07,2010.09) -> Newbler | #Fake read + 454(2007.06,07,2010.09) -> Newbler | ||
=Read Libraries= | =Read Libraries= | ||
| - | *Illumina PE - 2007 | + | *Illumina PE - 2007 8,046,794 X 2 |
| - | *454 - 2007.06 | + | *454 - 2007.06 SE 249,640, 264,032 |
| - | *454 - 2007.07 | + | *454 - 2007.07 SE 183,870, 187,022 |
| - | *454 - 2010.09 | + | *454 - 2010.09 PE 235,916 |
| + | *fake reads SE 15,379 | ||
| + | [[File:V S 6 1.png|1000px]] | ||
| + | =Primers for gap filling= | ||
| + | [[Primer_Verrucosispora_gap]] | ||
| + | =rRNA operon= | ||
| + | *copy number: 3 | ||
| + | **5s : all same | ||
| + | **16s,23s : all different | ||
| + | =One plasmid= | ||
| + | *length: 5.8 kb | ||
| + | *[[Verr_Origin|Origin]] | ||
| + | =Sigletons= | ||
| + | Singletons | ||
| + | *454 | ||
| + | grep Singleton 454ReadStatus.txt > singles.txt | ||
| + | sfffile -o singles.sff -i singles.txt ~/db/genome/Verrucosispora/SEP_2010_PE/GN0TVDJ01.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_06_22_19_39_57_FLX03070147_adminrig_STACH01/D_2007_06_22_19_39_57_FLX03070147_adminrig_OTFAnalysis/sff/EQ4OWVR01.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_06_22_19_39_57_FLX03070147_adminrig_STACH01/D_2007_06_22_19_39_57_FLX03070147_adminrig_OTFAnalysis/sff/EQ4OWVR02.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_07_13_18_06_24_FLX03070147_adminrig_Stach02/D_2007_07_13_18_06_24_FLX03070147_adminrig_OTFAnalysis/sff/ESA5WYK01.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_07_13_18_06_24_FLX03070147_adminrig_Stach02/D_2007_07_13_18_06_24_FLX03070147_adminrig_OTFAnalysis/sff/ESA5WYK02.sff | ||
| + | sffinfo -s singles.sff > singles.fna | ||
| + | sffinfo -q singles.sff > singles.qual | ||
| + | *solexa | ||
| + | maq | ||
| + | =Submission= | ||
| + | *check tool id1: JSID_01_45_130.14.22.21_9000 | ||
| + | *check tool id2: JSID_01_46_130.14.22.21_9000 | ||
| + | *check tool id3: JSID_01_47_130.14.22.21_9000 | ||
Latest revision as of 10:27, 22 June 2011
Verrucosispora sp.
Contents |
Circular view
Log
- Illuminia PE -> ABySS -> Fake reads
- Fake read + 454(2007.06,07) -> Newbler
- Fake read + 454(2007.06,07,2010.09) -> Newbler
Read Libraries
- Illumina PE - 2007 8,046,794 X 2
- 454 - 2007.06 SE 249,640, 264,032
- 454 - 2007.07 SE 183,870, 187,022
- 454 - 2010.09 PE 235,916
- fake reads SE 15,379
Primers for gap filling
rRNA operon
- copy number: 3
- 5s : all same
- 16s,23s : all different
One plasmid
- length: 5.8 kb
- Origin
Sigletons
Singletons
- 454
grep Singleton 454ReadStatus.txt > singles.txt sfffile -o singles.sff -i singles.txt ~/db/genome/Verrucosispora/SEP_2010_PE/GN0TVDJ01.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_06_22_19_39_57_FLX03070147_adminrig_STACH01/D_2007_06_22_19_39_57_FLX03070147_adminrig_OTFAnalysis/sff/EQ4OWVR01.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_06_22_19_39_57_FLX03070147_adminrig_STACH01/D_2007_06_22_19_39_57_FLX03070147_adminrig_OTFAnalysis/sff/EQ4OWVR02.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_07_13_18_06_24_FLX03070147_adminrig_Stach02/D_2007_07_13_18_06_24_FLX03070147_adminrig_OTFAnalysis/sff/ESA5WYK01.sff ~/db/genome/Verrucosispora/verrucosispora_jem/R_2007_07_13_18_06_24_FLX03070147_adminrig_Stach02/D_2007_07_13_18_06_24_FLX03070147_adminrig_OTFAnalysis/sff/ESA5WYK02.sff sffinfo -s singles.sff > singles.fna sffinfo -q singles.sff > singles.qual
- solexa
maq
Submission
- check tool id1: JSID_01_45_130.14.22.21_9000
- check tool id2: JSID_01_46_130.14.22.21_9000
- check tool id3: JSID_01_47_130.14.22.21_9000
