Pseudomonas aeruginosa: Difference between revisions
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3. 2007_1204_AMOSCmp-PA14 | 3. 2007_1204_AMOSCmp-PA14 | ||
4. '''2007_1204_AMOSCmp-PA14-relaxed -> best''' | 4. '''2007_1204_AMOSCmp-PA14-relaxed -> best''' | ||
5. 2007_1204_AMOSCmp-PA14-relaxed-noN : removed all reads that contain N's; same parameters as 2007_1204_AMOSCmp-PA14-relaxed => no big differences compared to 2007_1204_AMOSCmp-PA14-relaxed | 5. 2007_1210_AMOSCmp_PA7-relaxed | ||
6. 2007_1204_AMOSCmp-PA14-relaxed-noN (not shown): removed all reads that contain N's; same parameters as 2007_1204_AMOSCmp-PA14-relaxed => no big differences compared to 2007_1204_AMOSCmp-PA14-relaxed | |||
QC stats: | QC stats: | ||
Assembly 1 2 3 4 | Assembly 1 2 3 4 5 | ||
====================================================================================== | =================================================================================================== | ||
[Info] | [Info] | ||
REF PAO1 PAO1 PA14 PA14 | REF PAO1 PAO1 PA14 PA14 PA7 | ||
MINCLUSTER 20 20 20 20 | MINCLUSTER 20 20 20 20 20 | ||
MINOVL 10 3 10 3 | MINOVL 10 3 10 3 3 | ||
MAJORITY 70 50 70 50 | MAJORITY 70 50 70 50 50 | ||
MINMATCH 20 20 20 20 20 | |||
[Scaffolds] | [Scaffolds] | ||
TotalScaffolds 1 1 1 1 | TotalScaffolds 1 1 1 1 1 | ||
TotalContigsInScaffolds 4412 2197 3226 1828 | TotalContigsInScaffolds 4412 2197 3226 1828 25419 | ||
MeanContigsPerScaffold 4412 2197 3226 1828 | MeanContigsPerScaffold 4412 2197 3226 1828 25419 | ||
MinContigsPerScaffold 4412 2197 3226 1828 | MinContigsPerScaffold 4412 2197 3226 1828 25419 | ||
MaxContigsPerScaffold 4412 2197 3226 1828 | MaxContigsPerScaffold 4412 2197 3226 1828 25419 | ||
TotalBasesInScaffolds 6000280 5985597 6137031 6127761 | TotalBasesInScaffolds 6000280 5985597 6137031 6127761 4924485 | ||
MeanBasesInScaffolds 6000280 5985597 6137031 6127761 | MeanBasesInScaffolds 6000280 5985597 6137031 6127761 4924485 | ||
MaxBasesInScaffolds 6000280 5985597 6137031 6127761 | MaxBasesInScaffolds 6000280 5985597 6137031 6127761 4924485 | ||
N50ScaffoldBases 6000280 5985597 6137031 6127761 | N50ScaffoldBases 6000280 5985597 6137031 6127761 4924485 | ||
TotalSpanOfScaffolds 6264430 6264430 6537674 6537674 | TotalSpanOfScaffolds 6264430 6264430 6537674 6537674 6588355 | ||
MeanSpanOfScaffolds 6264430 6264430 6537674 6537674 | MeanSpanOfScaffolds 6264430 6264430 6537674 6537674 6588355 | ||
MinScaffoldSpan 6264430 6264430 6537674 6537674 | MinScaffoldSpan 6264430 6264430 6537674 6537674 6588355 | ||
MaxScaffoldSpan 6264430 6264430 6537674 6537674 | MaxScaffoldSpan 6264430 6264430 6537674 6537674 6588355 | ||
IntraScaffoldGaps 4411 2196 3225 1827 | IntraScaffoldGaps 4411 2196 3225 1827 25418 | ||
2KbScaffolds 1 1 1 1 | 2KbScaffolds 1 1 1 1 1 | ||
2KbScaffoldSpan 6264430 6264430 6537674 6537674 | 2KbScaffoldSpan 6264430 6264430 6537674 6537674 6588355 | ||
2KbScaffoldPercent 100 100 100 100 | 2KbScaffoldPercent 100 100 100 100 100 | ||
MeanSequenceGapSize 59 126 123 223 | MeanSequenceGapSize 59 126 123 223 64 | ||
[Contigs] | [Contigs] | ||
TotalContigs 4412 2197 3226 1828 | TotalContigs 4412 2197 3226 1828 25419 | ||
TotalBasesInContigs 6620035 6602214 6791916 6782045 | TotalBasesInContigs 6620035 6602214 6791916 6782045 5334464 | ||
MeanContigSize 1500 3005 2105 3710 | MeanContigSize 1500 3005 2105 3710 210 | ||
MinContigSize 33 33 33 33 | MinContigSize 33 33 33 33 33 | ||
MaxContigSize 21576 46268 61425 86811 | MaxContigSize 21576 46268 61425 86811 13454 | ||
N50ContigBases 3548 8478 6480 14280 | N50ContigBases 3548 8478 6480 14280 410 | ||
[BigContigs_greater_10000] | [BigContigs_greater_10000] | ||
TotalBigContigs 44 173 142 229 | TotalBigContigs 44 173 142 229 3 | ||
BigContigLength 547699 2709766 2127747 4558923 | BigContigLength 547699 2709766 2127747 4558923 34975 | ||
MeanBigContigSize 12448 15663 14984 19908 | MeanBigContigSize 12448 15663 14984 19908 11658 | ||
MinBigContig 10018 10045 10022 10040 | MinBigContig 10018 10045 10022 10040 10262 | ||
MaxBigContig 21576 46268 61425 86811 | MaxBigContig 21576 46268 61425 86811 13454 | ||
BigContigsPercentBases 8 41 31 67 | BigContigsPercentBases 8 41 31 67 0.66 | ||
[SmallContigs] | [SmallContigs] | ||
TotalSmallContigs 4368 2024 3084 1599 | TotalSmallContigs 4368 2024 3084 1599 25416 | ||
SmallContigLength 6072336 3892448 4664169 2223122 | SmallContigLength 6072336 3892448 4664169 2223122 5299489 | ||
MeanSmallContigSize 1390 1923 1512 1390 | MeanSmallContigSize 1390 1923 1512 1390 209 | ||
MinSmallContig 33 33 33 33 | MinSmallContig 33 33 33 33 33 | ||
MaxSmallContig 9964 9996 9977 9995 | MaxSmallContig 9964 9996 9977 9995 8411 | ||
SmallContigsPercentBases 92 59 69 33 | SmallContigsPercentBases 92 59 69 33 99 | ||
[Reads] | [Reads] | ||
TotalReads 8627900 8627900 8627900 8627900 | TotalReads 8627900 8627900 8627900 8627900 8627900 | ||
ReadsInContigs 6218126 6218255 6541160 6541364 | ReadsInContigs 6218126 6218255 6541160 6541364 3766798 | ||
BigContigReads 549658 2601986 2115038 4460608 | BigContigReads 549658 2601986 2115038 4460608 39074 | ||
SmallContigReads 5668468 3616269 4426122 2080756 | SmallContigReads 5668468 3616269 4426122 2080756 3727724 | ||
SingletonReads 2409774 2409645 2086740 2086536 | SingletonReads 2409774 2409645 2086740 2086536 4861102 | ||
=== 2007_1204_AMOSCmp-PA14-relaxed -> best: 1828 contigs === | === 2007_1204_AMOSCmp-PA14-relaxed -> best: 1828 contigs === | ||
Revision as of 19:27, 10 December 2007
Strain PA-b1
Data
NCBI
Complete strains:
PAO1 AE004091 1 chromosome, 6,264,404 bp, 66.56 %GC PA14 CP000438 1 chromosome, 6,537,648 bp, 66.29 %GC PA7 CP000744 1 chromosome, 6588339 bp
CBCB
File location:
/fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/
Files:
s_1_0001_prb.txt s_1_sequence.txt # contains seq & qual s_1_tag.txt s_7_0300_prb.txt s_7_sequence.txt # contains seq & qual s_7_tag.txt wc -l s_1_sequence.txt s_7_sequence.txt 4105993 s_1_sequence.txt 4521907 s_7_sequence.txt 8627900 total
grep -c N s_*seq s_1_sequence.seq:37933 s_7_sequence.seq:69669
Assemblies
CBCB
1. 2007_1203_AMOSCmp-PAO1 2. 2007_1203_AMOSCmp-PAO1-relaxed 3. 2007_1204_AMOSCmp-PA14 4. 2007_1204_AMOSCmp-PA14-relaxed -> best 5. 2007_1210_AMOSCmp_PA7-relaxed 6. 2007_1204_AMOSCmp-PA14-relaxed-noN (not shown): removed all reads that contain N's; same parameters as 2007_1204_AMOSCmp-PA14-relaxed => no big differences compared to 2007_1204_AMOSCmp-PA14-relaxed
QC stats:
Assembly 1 2 3 4 5 ===================================================================================================
[Info] REF PAO1 PAO1 PA14 PA14 PA7 MINCLUSTER 20 20 20 20 20 MINOVL 10 3 10 3 3 MAJORITY 70 50 70 50 50 MINMATCH 20 20 20 20 20
[Scaffolds] TotalScaffolds 1 1 1 1 1 TotalContigsInScaffolds 4412 2197 3226 1828 25419 MeanContigsPerScaffold 4412 2197 3226 1828 25419 MinContigsPerScaffold 4412 2197 3226 1828 25419 MaxContigsPerScaffold 4412 2197 3226 1828 25419 TotalBasesInScaffolds 6000280 5985597 6137031 6127761 4924485 MeanBasesInScaffolds 6000280 5985597 6137031 6127761 4924485 MaxBasesInScaffolds 6000280 5985597 6137031 6127761 4924485 N50ScaffoldBases 6000280 5985597 6137031 6127761 4924485 TotalSpanOfScaffolds 6264430 6264430 6537674 6537674 6588355 MeanSpanOfScaffolds 6264430 6264430 6537674 6537674 6588355 MinScaffoldSpan 6264430 6264430 6537674 6537674 6588355 MaxScaffoldSpan 6264430 6264430 6537674 6537674 6588355 IntraScaffoldGaps 4411 2196 3225 1827 25418 2KbScaffolds 1 1 1 1 1 2KbScaffoldSpan 6264430 6264430 6537674 6537674 6588355 2KbScaffoldPercent 100 100 100 100 100 MeanSequenceGapSize 59 126 123 223 64
[Contigs] TotalContigs 4412 2197 3226 1828 25419 TotalBasesInContigs 6620035 6602214 6791916 6782045 5334464 MeanContigSize 1500 3005 2105 3710 210 MinContigSize 33 33 33 33 33 MaxContigSize 21576 46268 61425 86811 13454 N50ContigBases 3548 8478 6480 14280 410
[BigContigs_greater_10000] TotalBigContigs 44 173 142 229 3 BigContigLength 547699 2709766 2127747 4558923 34975 MeanBigContigSize 12448 15663 14984 19908 11658 MinBigContig 10018 10045 10022 10040 10262 MaxBigContig 21576 46268 61425 86811 13454 BigContigsPercentBases 8 41 31 67 0.66
[SmallContigs] TotalSmallContigs 4368 2024 3084 1599 25416 SmallContigLength 6072336 3892448 4664169 2223122 5299489 MeanSmallContigSize 1390 1923 1512 1390 209 MinSmallContig 33 33 33 33 33 MaxSmallContig 9964 9996 9977 9995 8411 SmallContigsPercentBases 92 59 69 33 99
[Reads] TotalReads 8627900 8627900 8627900 8627900 8627900 ReadsInContigs 6218126 6218255 6541160 6541364 3766798 BigContigReads 549658 2601986 2115038 4460608 39074 SmallContigReads 5668468 3616269 4426122 2080756 3727724 SingletonReads 2409774 2409645 2086740 2086536 4861102
2007_1204_AMOSCmp-PA14-relaxed -> best: 1828 contigs
Find adjacent contigs:
1. nucmer contigs, filter adjacent contig end matches
overlaps haev to be >=20 bp => 12 overlaps
$ nucmer -c 20 -l 20 /fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/Assembly/2007_1204_AMOSCmp-PA14-relaxed/nucmer/Pa.fasta /fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/Assembly/2007_1204_AMOSCmp-PA14-relaxed/nucmer/Pa.fasta ...
[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [LEN R] [LEN Q] | [COV R] [COV Q] | [TAGS]
===============================================================================================================================
6738 6765 | 1 28 | 28 28 | 100.00 | 6765 41748 | 0.41 0.07 | 1132 1133 [END]
133 161 | 1 29 | 29 29 | 100.00 | 161 10235 | 18.01 0.28 | 1271 1272 [END]
11534 11631 | 1 98 | 98 98 | 92.86 | 11631 3390 | 0.84 2.89 | 1409 1410 [END]
102 122 | 1 21 | 21 21 | 100.00 | 122 46 | 17.21 45.65 | 1464 1465 [END]
281 301 | 1 21 | 21 21 | 100.00 | 301 183 | 6.98 11.48 | 1623 1624 [END]
659 988 | 1 303 | 330 303 | 79.15 | 988 418 | 33.40 72.49 | 1626 1627 [END]
177 416 | 5 241 | 240 237 | 75.93 | 418 1604 | 57.42 14.78 | 1627 1628 [END]
1296 1344 | 1 49 | 49 49 | 100.00 | 1344 15090 | 3.65 0.32 | 217 218 [END]
319 652 | 1 212 | 334 212 | 60.30 | 652 322 | 51.23 65.84 | 314 315 [END]
13265 13285 | 1 21 | 21 21 | 100.00 | 13285 14465 | 0.16 0.15 | 757 758 [END]
892 995 | 5 176 | 104 172 | 59.30 | 1000 3085 | 10.40 5.58 | 815 816 [END]
2406 2425 | 1 20 | 20 20 | 100.00 | 2425 5200 | 0.82 0.38 | 93 94 [END]
2. nucmer PA14 contigs to PAO1 contigs