Info - bacterium SCGC AAA003-K10

Seq. Project name:

bacterium SCGC AAA003-K10 ( Project ID: 1014110 )

Product:

Microbial Minimal Draft, Single Cell

Proposal Name:

Dark ocean microbial single cell genomics (Proposal ID: 620)

Project PI:

Ramunas Stepanauskas

User Program:

CSP

Program Year:

2012

Scientific Program:

Microbial

Related Projects:

FD 1014109; SP 1014110; AP 1092684

Release Date:

2017-12-13

Organism
Genus/species/strain/isolate:	bacterium SCGC AAA003-K10 / SCGC AAA003-K10 / SCGC AAA003-K10
GOLD ID:	Gp0032094

Data Submission

NCBI BioProject ID:	195874
NCBI Tax ID:	939720
SRA accession:	SRP025090 (2013-06-11)

Contacts
JGI:	[email protected]
Request DNA:	Ramunas Stepanauskas <[email protected]>

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1014110 Gemmatimonadetes bacterium SCGC AAA003-K10 1) RAW DATA: LibraryName NumReads ReadType ReadType FileName LIB 18532548 2x157 Illumina Std PE (cassava 1.8) 6669.2.51254.GCCAAT.fastq 2) ILLUMINA STD PE 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: 18532548 (100%) Num contam reads removed: 10 (0.0%) - human_chr2 2 0.00% - human_chr13 1 0.00% - human_chr11 1 0.00% - human_chr15 1 0.00% Artifact reads removed: 95362 (0.5%) Normalized reads removed: 18025588 (97.3%) Total reads removed: 18120960 (97.8%) Total reads remaining: 411588 (2.2%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 18532548 (100%) Num contam reads identified: 0 (0.0%) 4) ASSEMBLY STATS: a) IDBA-UD: Avg GC Content: 56.28 +/- 4.23% Largest Contig: 59.1 KB Main genome scaffold total: 540 Main genome contig total: 540 Main genome scaffold sequence total: 1.9 MB Main genome contig sequence total: 1.9 MB (-> 0.0% gap) Main genome scaffold N/L50: 53/9.2 KB Main genome contig N/L50: 53/9.2 KB Number of scaffolds > 50 KB: 1 % main genome in scaffolds > 50 KB: 3.1% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 540 540 1,895,424 1,895,424 100.00% 1 kb 279 279 1,759,173 1,759,173 100.00% 2.5 kb 188 188 1,612,440 1,612,440 100.00% 5 kb 113 113 1,337,536 1,337,536 100.00% 10 kb 42 42 845,852 845,852 100.00% 25 kb 9 9 343,371 343,371 100.00% 50 kb 1 1 59,063 59,063 100.00% b) Allpaths + IDBA-UD simulated read pairs: Assembly stats of the ALLPATHS assembly. The input contains simulated 1-3 kb read pairs created from the IDBA-UD assembly and reads that have been filtered for contamination, artifacts and normalized. Avg GC Content: 57.14 +/- 3.27% Largest Contig: 93.3 KB Main genome scaffold total: 112 Main genome contig total: 112 Main genome scaffold sequence total: 1.7 MB Main genome contig sequence total: 1.7 MB (-> 0.0% gap) Main genome scaffold N/L50: 18/26.7 KB Main genome contig N/L50: 18/26.7 KB Number of scaffolds > 50 KB: 4 % main genome in scaffolds > 50 KB: 19.1% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 112 112 1,666,023 1,666,023 100.00% 1 kb 112 112 1,666,023 1,666,023 100.00% 2.5 kb 100 100 1,638,674 1,638,674 100.00% 5 kb 81 81 1,573,236 1,573,236 100.00% 10 kb 49 49 1,339,935 1,339,935 100.00% 25 kb 21 21 924,307 924,307 100.00% 50 kb 4 4 318,109 318,109 100.00% 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) IDBA-UD assembly step for creating simulated read pairs: IDBA-UD version: 1.0.9 IDBA-UD params: --no_local e) ALLPATHS assembly step: ALLPATHS version: r42328 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,1,260,35,,,inward,0,0 SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0 6) WORKFLOW STEPS: 1. Removed contamination (human contaminants). 2. Removed illumina artifacts (synthetic oligos used in the laboratory). 3. Normalized read coverage. 4. Created IDBA-UD assembly of the contam+artifact+normalized filtered data. 5. Created simulated 1-3 kb read pairs using IDBA-UD contigs from step 4. 6. Created allpaths assembly using IDBA-UD simulated read pairs (step 5) and the contam+artifact+normalized filtered data. 7) ASSEMBLERS USED: IDBA-UD, AllpathsLG 8) RELEASE DATE: Wed Apr 3 14:16:48 PDT 2013 By Alexander Spunde- [email protected] 9) 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 2.1.2.1).

General Information

QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 
1014110
Gemmatimonadetes bacterium SCGC AAA003-K10

1) RAW DATA:

LibraryName	NumReads	ReadType	ReadType	FileName
LIB	18532548	2x157	Illumina Std PE (cassava 1.8)	6669.2.51254.GCCAAT.fastq

2) ILLUMINA STD PE 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:          18532548 (100%)
Num contam reads removed:   10 (0.0%)
  - human_chr2 	2	0.00%
  - human_chr13	1	0.00%
  - human_chr11	1	0.00%
  - human_chr15	1	0.00%
Artifact reads removed:     95362 (0.5%)
Normalized reads removed:   18025588 (97.3%)
Total reads removed:        18120960 (97.8%)
Total reads remaining:      411588 (2.2%)

3) ILLUMINA STD PE READ IDENTIFICATION STATS

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

Total input reads:           18532548 (100%)
Num contam reads identified: 0 (0.0%)

4) ASSEMBLY STATS:

a) IDBA-UD:
Avg GC Content: 56.28 +/- 4.23%

Largest Contig: 59.1 KB

Main genome scaffold total: 540
Main genome contig total:   540
Main genome scaffold sequence total: 1.9 MB
Main genome contig sequence total:   1.9 MB (->  0.0% gap)
Main genome scaffold N/L50: 53/9.2 KB
Main genome contig N/L50:   53/9.2 KB
Number of scaffolds > 50 KB: 1
% main genome in scaffolds > 50 KB:  3.1%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       540        540    1,895,424    1,895,424   100.00%
   1 kb       279        279    1,759,173    1,759,173   100.00%
 2.5 kb       188        188    1,612,440    1,612,440   100.00%
   5 kb       113        113    1,337,536    1,337,536   100.00%
  10 kb        42         42      845,852      845,852   100.00%
  25 kb         9          9      343,371      343,371   100.00%
  50 kb         1          1       59,063       59,063   100.00%

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

Avg GC Content: 57.14 +/- 3.27%

Largest Contig: 93.3 KB

Main genome scaffold total: 112
Main genome contig total:   112
Main genome scaffold sequence total: 1.7 MB
Main genome contig sequence total:   1.7 MB (->  0.0% gap)
Main genome scaffold N/L50: 18/26.7 KB
Main genome contig N/L50:   18/26.7 KB
Number of scaffolds > 50 KB: 4
% main genome in scaffolds > 50 KB: 19.1%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       112        112    1,666,023    1,666,023   100.00%
   1 kb       112        112    1,666,023    1,666,023   100.00%
 2.5 kb       100        100    1,638,674    1,638,674   100.00%
   5 kb        81         81    1,573,236    1,573,236   100.00%
  10 kb        49         49    1,339,935    1,339,935   100.00%
  25 kb        21         21      924,307      924,307   100.00%
  50 kb         4          4      318,109      318,109   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) IDBA-UD assembly step for creating simulated read pairs:
IDBA-UD version: 1.0.9
IDBA-UD params: --no_local

e) ALLPATHS assembly step:
ALLPATHS version: r42328
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,1,260,35,,,inward,0,0
SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0

6) WORKFLOW STEPS:
1. Removed contamination (human contaminants).
2. Removed illumina artifacts (synthetic oligos used in the laboratory).
3. Normalized read coverage.
4. Created IDBA-UD assembly of the contam+artifact+normalized filtered data.
5. Created simulated 1-3 kb read pairs using IDBA-UD contigs from step 4.
6. Created allpaths assembly using IDBA-UD simulated read pairs (step 5) and the contam+artifact+normalized filtered data.

7) ASSEMBLERS USED:
IDBA-UD, AllpathsLG

8) RELEASE DATE:
Wed Apr  3 14:16:48 PDT 2013 By Alexander Spunde- [email protected]

9) 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 2.1.2.1).


								

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.