Helicobacter pylori
Jump to navigation
Jump to search
Data
Wustl
- http://gordonlab.wustl.edu/MengWu/WU_JBC_2009.html
- http://pathogenomics.bham.ac.uk/blog/2009/09/tips-for-de-novo-bacterial-genome-assembly/
- http://www.jbc.org/content/early/2009/09/01/jbc.M109.052738.abstract
NCBI complete genomes
- Genome info
id len gc%
1 NC_000915.1 1667867 38.87 Helicobacter pylori 26695
2 NC_000921.1 1643831 39.19 Helicobacter pylori J99
3 NC_008086.1 1596366 39.08 Helicobacter pylori HPAG1
4 NC_010698.2 1608548 38.91 Helicobacter pylori Shi470
5 NC_011333.1 1652982 38.89 Helicobacter pylori G27
6 NC_011498.1 1673813 38.81 Helicobacter pylori P12
7 NC_012973.1 1576758 39.16 Helicobacter pylori B38
- Alignment info (NC_000915 0cvg regions)
. elem min q1 q2 q3 max mean n50 sum
1 NC_000915-NC_000915 . . . . . . . . .
2 NC_000915-NC_000921 197 2 81 203 495 17816 644 2146 126988
3 NC_000915-NC_008086 151 3 103 242 894 26862 951 3103 143652
4 NC_000915-NC_010698 206 2 115 283 706 12779 726 1941 149744
5 NC_000915-NC_011333 138 2 111 260 695 7457 688 1941 95063
6 NC_000915-NC_011498 157 2 83 185 565 5362 505 1357 79337
7 NC_000915-NC_012973 140 2 108 239 526 37389 1018 5729 142568
NCBI SRA
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&term=SRP001104 (24 data sets; 10 not loaded)
- http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP001104
Assemblies
Wustl
. . ctgs min q1 q2 q3 max mean n50 sum reads
1 HPKX_1039_AG0C1.scarf.assembled-29-21 233 100 318 1700 9639 77743 7085 19912 1650899 0
2 HPKX_1039_AG0C2.solexa.txt.assembled-23-12 420 101 341 1684 5301 36588 3914 9412 1644043 5.2M
3 HPKX_1039_AG4C1.scarf.assembled-27-22 271 100 217 1421 8273 90368 6115 17093 1657230 0
4 HPKX_1039_AG4C2.solexa.txt.assembled-25-12 365 100 301 1595 5658 51523 4522 11890 1650547 6.8M
5 HPKX_1172_AG0C1_090424.solexa.txt.assembled-25-30 217 107 557 3370 10683 58848 7099 15527 1540507 8.6M
6 HPKX_1172_AG0C2_2lanes.assembled-21-8 1170 100 264 717 1768 11444 1319 2661 1543511 7.2M
7 HPKX_1172_AG4C1_090424.solexa.txt.assembled-23-20 377 103 355 2178 6166 35180 4169 9160 1571948 8.5M
8 HPKX_1172_AG4C2.solexa.txt.assembled-25-15 317 100 274 1540 6256 37505 4987 14946 1581161 6.0M
9 HPKX_1259_NL0C1.scarf.assembled-21-17 1704 100 264 598 1274 7953 936 1606 1595297 0
10 HPKX_1259_NL0C2.solexa.txt.assembled-23-12 410 102 240 928 4863 32792 3882 11295 1591864 3.6M
11 HPKX_1259_NL4C1.scarf.assembled-27-23 283 100 224 1098 6814 98400 5634 18624 1594699 0
12 HPKX_1259_NL4C2.solexa.txt.assembled-23-12 455 102 222 874 4348 32792 3520 11010 1601950 6.3M
13 HPKX_1379_NL0C1.scarf.assembled-27-22 295 100 230 1243 7551 59556 5539 15858 1634019 0
14 HPKX_1379_NL0C2.solexa.txt.assembled-23-12 416 100 216 1000 5177 53581 3931 11219 1635644 6.3M
15 HPKX_1379_NL4C1.scarf.assembled-25-23 328 100 227 1084 6601 61090 4996 14203 1638925 0
16 HPKX_1379_NL4C2.solexa.txt.assembled-25-20 291 100 231 1501 6751 64227 5539 15080 1612046 4.6M
17 HPKX_345_AG4C1.scarf.assembled-27-22 251 100 241 1272 8265 97643 6534 19718 1640151 0
18 HPKX_345_NL0C1.scarf.assembled-25-30 305 100 243 1146 6718 59632 5360 15874 1634815 0
19 HPKX_345_NL0C2_090424.solexa.txt.assembled-25-26 283 100 254 2009 8300 59229 5629 13524 1593064 11.1M
20 HPKX_438_AG0C1.scarf.assembled-27-25 267 100 348 1710 8311 87876 6071 16918 1620975 0M
21 HPKX_438_AG0C2.solexa.txt.assembled-23-18 407 102 396 1777 5455 31183 3963 8830 1613167 6.3M
22 HPKX_438_CA4C1.scarf.assembled-27-26 237 100 348 1580 8856 97139 6845 19582 1622487 0
23 HPKX_438_CA4C2.solexa.txt.assembled-23-11 485 101 363 1502 4408 35471 3332 7779 1616183 4.1M
24 HPKX_345_AG4C2 . 12.1M
CBCB
23 HPKX_438_CA4C2.solexa.txt.assembled-23-11
Velvet:
- Fastq vs Fasta: no diffrence
- "velvetg . -exp_cov 80" vs "velvetg . -exp_cov auto" slightly worse
Kmers:
meryl -C -B -m 12 -s prefix.seq -o prefix.12mers meryl -Dh -s prefix.12mers | sort -nk2 -r | more