Info - Cyanobacteria bacterium SCGC JGI 014-E08

Seq. Project name:

Cyanobacteria bacterium SCGC JGI 014-E08 ( Project ID: 406790 )

Product:

Standard Draft

Proposal Name:

Unraveling the unique microbial diversity of the Etoliko lagoon in Western Greece through a single cell genomics approach (Proposal ID: 335)

Project PI:

George Tsiamis

User Program:

CSP

Program Year:

2011

Scientific Program:

Microbial

Genome Portal:

2265123001

Related Projects:

FD 1080385; SP 406790; AP 1423621

Release Date:

2012-05-25

Organism
Genus/species/strain/isolate:	Cyanobacteria bacterium SCGC JGI 0000014-E08 / SCGC JGI 0000014-E08 /
GOLD ID:	Gp0015821

Data Submission

NCBI BioProject ID:	165539
NCBI Tax ID:	1130364

Contacts
JGI:	[email protected]
Request DNA:	George Tsiamis <[email protected]>

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 4096683 Cyanobacteria bacterium JGI 0000014-E08 1) RAW DATA: LibraryName NumReads ReadType FileName INYB 22669248 2x150 2259.4.1848.GAGTGG.fastq 2) STD READ FILTERING STATS: Reads were screened against human contaminants, synthetic oligos used in the Illumina sequencing process and normalized. Pairs of matching reads were removed from the dataset. Total input reads: 22669248 (100%) Num contam reads removed: 4 (0.0%) - human_chr2 2 0.00% - human_chr15 2 0.00% Artifact reads removed: 76920 (0.3%) Normalized reads removed: 22512166 (99.3%) Total reads removed: 22589090 (99.6%) Total reads remaining: 80158 (0.4%) 3) STD READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 22669248 (100%) Num contam reads identified: 0 (0.0%) 4) ASSEMBLY STATS: a) Velvet assembly using VelvetOptimizer: Assembly stats of the Velvet assembly created by the velvet optimizer. The input reads have been filtered for contamination, artifacts and normalized. Avg GC Content: 42.59 +/- 8.94% Largest Contig: 29.9 KB Main genome scaffold total: 116 Main genome contig total: 139 Main genome scaffold sequence total: 364.9 KB Main genome contig sequence total: 361.9 KB (-> 0.5% gap) Main genome scaffold N/L50: 14/8.7 KB Main genome contig N/L50: 15/6.8 KB Number of scaffolds > 50 KB: 0 % main genome in scaffolds > 50 KB: 0.0% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 116 139 364,948 361,934 99.17% 1 kb 61 80 328,387 325,696 99.18% 2.5 kb 33 46 287,791 285,822 99.32% 5 kb 23 31 251,898 250,583 99.48% 10 kb 9 11 143,199 142,690 99.64% 25 kb 1 1 29,919 29,859 99.80% b) Allpaths + Velvet simulated read pairs: Assembly stats of the ALLPATHS assembly. The input contains simulated 1-3 kb read pairs created from the Velvet assembly and reads that have been filtered for contamination, artifacts and normalized. Avg GC Content: 45.43 +/- 8.90% Largest Contig: 24.0 KB Main genome scaffold total: 58 Main genome contig total: 58 Main genome scaffold sequence total: 326.8 KB Main genome contig sequence total: 326.8 KB (-> 0.0% gap) Main genome scaffold N/L50: 13/8.9 KB Main genome contig N/L50: 13/8.9 KB Number of scaffolds > 50 KB: 0 % main genome in scaffolds > 50 KB: 0.0% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 58 58 326,785 326,785 100.00% 1 kb 58 58 326,785 326,785 100.00% 2.5 kb 34 34 288,583 288,583 100.00% 5 kb 23 23 247,099 247,099 100.00% 10 kb 8 8 125,274 125,274 100.00% c) Merged Allpaths and optimized Velvet assemblies: Assembly stats of the final assembly. This assembly was performed using a hybrid of the ALLPATHS (referenced above) and Velvet optimized assemblies. The Velvet optimized assemblies were performed using reads that have been filtered for contamination, artifact and normalized. These assemblies were chosen based on the best kmer based on largest contig lengths and varying coverage cutoffs. The contigs of the velvet assemblies and the ALLPATHS assembly were merged and unique sequences selected. Avg GC Content: 44.38 +/- 8.58% Largest Contig: 24.9 KB Main genome scaffold total: 83 Main genome contig total: 83 Main genome scaffold sequence total: 343.4 KB Main genome contig sequence total: 343.4 KB (-> 0.0% gap) Main genome scaffold N/L50: 13/8.9 KB Main genome contig N/L50: 13/8.9 KB Number of scaffolds > 50 KB: 0 % main genome in scaffolds > 50 KB: 0.0% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 83 83 343,353 343,353 100.00% 1 kb 59 59 327,995 327,995 100.00% 2.5 kb 32 32 283,768 283,768 100.00% 5 kb 22 22 242,857 242,857 100.00% 10 kb 8 8 126,926 126,926 100.00% 5) KEY PIPELINE CMDS: a) Contamination removal step: Bwa version: 0.5.9-r16 Bwa aln params: Bwa sampe params: -A -P -s b) Artifact removal step: duk params: -k 22 -s 1 -c 1 c) Normalization step: kmernorm params: -k 21 -t 15 -c 2 d) Velvet assembly step for creating simulated read pairs: Velvet version: 1.1.04 Velvet optimizer version: 2.1.7 Velvet optimizer params: --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500" e) Simulated read pairing creation step: Wgsim version: 0.3.0 Wgsim params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0 f) ALLPATHS assembly step: ALLPATHS version: r41043 Contents of in_libs.csv: library_name, project_name, organism_name, type, paired, frag_size, frag_stddev, insert_size, insert_stddev, read_orientation, genomic_start, genomic_end STD_1,project,assembly,fragment,1,200,35,,,inward,0,0 SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0 g) Velvet assembly step (varying kmer and coverage cutoffs): Velvet version: 1.1.04 Best Kmer: 85 Best cutoff coverages: 1 5 auto 6) WORKFLOW STEPS: 1. Removed contamination (human contaminants). 2. Removed illumina artifacts (synthetic oligos used in the laboratory). 3. Normalized read coverage. 4. Created velvet assembly of the contam+artifact+normalized filtered data. 5. Created simulated 1-3 kb read pairs using velvet contigs from step 4. 6. Created allpaths assembly using velvet simulated read pairs (step 5) and the contam+artifact+normalized filtered data. 7. Ran multiple velvet assemblies at different kmer and coverage windows using the contam+artifact+normalized filtered data. Merged velvet contigs with allpaths contigs from step 6 and select only unique sequences. 7) RELEASE DATE: Thu May 17 09:36:38 PDT 2012 By Alexander Spunde- [email protected] 8) AUTHORS: For additional information, please contact: Stephan Trong - [email protected] James Han - [email protected] This file was automatically generated by the jigsaw pipeline software (version 2.0.1).

General Information

QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 
4096683
Cyanobacteria bacterium JGI 0000014-E08

1) RAW DATA:

LibraryName	NumReads	ReadType	FileName
INYB	22669248	2x150	2259.4.1848.GAGTGG.fastq


2) STD READ FILTERING STATS:

Reads were screened against human contaminants, synthetic oligos used
in the Illumina sequencing process and normalized. Pairs of matching
reads were removed from the dataset.

Total input reads:          22669248 (100%)
Num contam reads removed:   4 (0.0%)
  - human_chr2 	2	0.00%
  - human_chr15	2	0.00%
Artifact reads removed:     76920 (0.3%)
Normalized reads removed:   22512166 (99.3%)
Total reads removed:        22589090 (99.6%)
Total reads remaining:      80158 (0.4%)

3) STD READ IDENTIFICATION STATS

This step identifies contaminants but does not remove them from the dataset.

Total input reads:           22669248 (100%)
Num contam reads identified: 0 (0.0%)

4) ASSEMBLY STATS:

a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer. The input reads have been filtered for contamination,
artifacts and normalized.

Avg GC Content: 42.59 +/- 8.94%

Largest Contig: 29.9 KB

Main genome scaffold total: 116
Main genome contig total:   139
Main genome scaffold sequence total: 364.9 KB
Main genome contig sequence total:   361.9 KB (->  0.5% gap)
Main genome scaffold N/L50: 14/8.7 KB
Main genome contig N/L50:   15/6.8 KB
Number of scaffolds > 50 KB: 0
% main genome in scaffolds > 50 KB:  0.0%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       116        139      364,948      361,934    99.17%
   1 kb        61         80      328,387      325,696    99.18%
 2.5 kb        33         46      287,791      285,822    99.32%
   5 kb        23         31      251,898      250,583    99.48%
  10 kb         9         11      143,199      142,690    99.64%
  25 kb         1          1       29,919       29,859    99.80%

b) Allpaths + Velvet simulated read pairs:
Assembly stats of the ALLPATHS assembly. The input contains simulated
1-3 kb read pairs created from the Velvet assembly and reads that
have been filtered for contamination, artifacts and normalized.

Avg GC Content: 45.43 +/- 8.90%

Largest Contig: 24.0 KB

Main genome scaffold total: 58
Main genome contig total:   58
Main genome scaffold sequence total: 326.8 KB
Main genome contig sequence total:   326.8 KB (->  0.0% gap)
Main genome scaffold N/L50: 13/8.9 KB
Main genome contig N/L50:   13/8.9 KB
Number of scaffolds > 50 KB: 0
% main genome in scaffolds > 50 KB:  0.0%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All        58         58      326,785      326,785   100.00%
   1 kb        58         58      326,785      326,785   100.00%
 2.5 kb        34         34      288,583      288,583   100.00%
   5 kb        23         23      247,099      247,099   100.00%
  10 kb         8          8      125,274      125,274   100.00%

c) Merged Allpaths and optimized Velvet assemblies:
Assembly stats of the final assembly. This assembly was performed
using a hybrid of the ALLPATHS (referenced above) and Velvet
optimized assemblies. The Velvet optimized assemblies were performed
using reads that have been filtered for contamination, artifact and
normalized. These assemblies were chosen based on the best kmer based
on largest contig lengths and varying coverage cutoffs. The contigs
of the velvet assemblies and the ALLPATHS assembly were merged and
unique sequences selected.

Avg GC Content: 44.38 +/- 8.58%

Largest Contig: 24.9 KB

Main genome scaffold total: 83
Main genome contig total:   83
Main genome scaffold sequence total: 343.4 KB
Main genome contig sequence total:   343.4 KB (->  0.0% gap)
Main genome scaffold N/L50: 13/8.9 KB
Main genome contig N/L50:   13/8.9 KB
Number of scaffolds > 50 KB: 0
% main genome in scaffolds > 50 KB:  0.0%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All        83         83      343,353      343,353   100.00%
   1 kb        59         59      327,995      327,995   100.00%
 2.5 kb        32         32      283,768      283,768   100.00%
   5 kb        22         22      242,857      242,857   100.00%
  10 kb         8          8      126,926      126,926   100.00%

5) KEY PIPELINE CMDS:

a) Contamination removal step:
Bwa version: 0.5.9-r16
Bwa aln params: 
Bwa sampe params: -A -P -s

b) Artifact removal step:
duk params: -k 22 -s 1 -c 1

c) Normalization step:
kmernorm params: -k 21 -t 15 -c 2

d) Velvet assembly step for creating simulated read pairs:
Velvet version: 1.1.04
Velvet optimizer version: 2.1.7
Velvet optimizer params: --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500"

e) Simulated read pairing creation step:
Wgsim version: 0.3.0
Wgsim params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0

f) ALLPATHS assembly step:
ALLPATHS version: r41043
Contents of in_libs.csv:
library_name, project_name, organism_name, type, paired, frag_size, frag_stddev, insert_size, insert_stddev, read_orientation, genomic_start, genomic_end
STD_1,project,assembly,fragment,1,200,35,,,inward,0,0
SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0

g) Velvet assembly step (varying kmer and coverage cutoffs):
Velvet version: 1.1.04
Best Kmer: 85
Best cutoff coverages:
1
5
auto

6) WORKFLOW STEPS:
1. Removed contamination (human contaminants).
2. Removed illumina artifacts (synthetic oligos used in the laboratory).
3. Normalized read coverage.
4. Created velvet assembly of the contam+artifact+normalized filtered data.
5. Created simulated 1-3 kb read pairs using velvet contigs from step 4.
6. Created allpaths assembly using velvet simulated read pairs (step 5) and the contam+artifact+normalized filtered data.
7. Ran multiple velvet assemblies at different kmer and coverage windows using the contam+artifact+normalized filtered data. Merged velvet contigs with allpaths contigs from step 6 and select only unique sequences.

7) RELEASE DATE:
Thu May 17 09:36:38 PDT 2012 By Alexander Spunde- [email protected]

8) AUTHORS:
For additional information, please contact:
Stephan Trong - [email protected]
James Han - [email protected]

This file was automatically generated by the jigsaw pipeline software (version 2.0.1).


								

Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Groups

This portal belongs to the following groups

##	Name	Type
1	Cyanobacteria