Info - Euryarchaeota archaeon SCGC AAA008-E08

Seq. Project name:

Euryarchaeota archaeon SCGC AAA008-E08 ( Project ID: 1014074 )

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 1014073; SP 1014074; AP 1092675

Release Date:

2017-12-13

Organism
Genus/species/strain/isolate:	Euryarchaeota archaeon SCGC AAA008-E08 / SCGC AAA008-E08 / SCGC AAA008-E08
GOLD ID:	Gp0032040

Data Submission

NCBI BioProject ID:	190846
NCBI Tax ID:	1298901
SRA accession:	SRP025055 (2013-06-11)

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

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1014074 Euryarchaeota archaeon AAA008-E08 1) RAW DATA: LibraryName NumReads ReadType ReadType FileName NPBS 21309734 2x157 Illumina Std PE (cassava 1.8) 6669.2.51254.CTTGTA.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: 21309734 (100%) Num contam reads removed: 4 (0.0%) - human_chr11 1 0.00% - human_chr12 1 0.00% Artifact reads removed: 3936 (0.0%) Normalized reads removed: 21058232 (98.8%) Total reads removed: 21062172 (98.8%) Total reads remaining: 247562 (1.2%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 21309734 (100%) Num contam reads identified: 2 (0.0%) - Escherichia 2 0.00% 4) ASSEMBLY STATS: a) IDBA-UD: Avg GC Content: 33.21 +/- 6.63% Largest Contig: 57.2 KB Main genome scaffold total: 272 Main genome contig total: 272 Main genome scaffold sequence total: 1.1 MB Main genome contig sequence total: 1.1 MB (-> 0.0% gap) Main genome scaffold N/L50: 29/9.8 KB Main genome contig N/L50: 29/9.8 KB Number of scaffolds > 50 KB: 1 % main genome in scaffolds > 50 KB: 5.2% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 272 272 1,093,484 1,093,484 100.00% 1 kb 172 172 1,038,642 1,038,642 100.00% 2.5 kb 108 108 934,481 934,481 100.00% 5 kb 58 58 760,609 760,609 100.00% 10 kb 27 27 535,199 535,199 100.00% 25 kb 6 6 207,060 207,060 100.00% 50 kb 1 1 57,218 57,218 100.00% 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: 31.50 +/- 4.09% Largest Contig: 98.3 KB Main genome scaffold total: 57 Main genome contig total: 57 Main genome scaffold sequence total: 1.0 MB Main genome contig sequence total: 1.0 MB (-> 0.0% gap) Main genome scaffold N/L50: 8/34.1 KB Main genome contig N/L50: 8/34.1 KB Number of scaffolds > 50 KB: 6 % main genome in scaffolds > 50 KB: 45.4% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 57 57 1,009,252 1,009,252 100.00% 1 kb 57 57 1,009,252 1,009,252 100.00% 2.5 kb 51 51 995,316 995,316 100.00% 5 kb 34 34 938,217 938,217 100.00% 10 kb 25 25 864,886 864,886 100.00% 25 kb 12 12 636,043 636,043 100.00% 50 kb 6 6 458,299 458,299 100.00% 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 14:09:47 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).

General Information

QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 
1014074
Euryarchaeota archaeon AAA008-E08

1) RAW DATA:

LibraryName	NumReads	ReadType	ReadType	FileName
NPBS	21309734	2x157	Illumina Std PE (cassava 1.8)	6669.2.51254.CTTGTA.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:          21309734 (100%)
Num contam reads removed:   4 (0.0%)
  - human_chr11	1	0.00%
  - human_chr12	1	0.00%
Artifact reads removed:     3936 (0.0%)
Normalized reads removed:   21058232 (98.8%)
Total reads removed:        21062172 (98.8%)
Total reads remaining:      247562 (1.2%)

3) ILLUMINA STD PE READ IDENTIFICATION STATS

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

Total input reads:           21309734 (100%)
Num contam reads identified: 2 (0.0%)
  - Escherichia	2	0.00%

4) ASSEMBLY STATS:

a) IDBA-UD:
Avg GC Content: 33.21 +/- 6.63%

Largest Contig: 57.2 KB

Main genome scaffold total: 272
Main genome contig total:   272
Main genome scaffold sequence total: 1.1 MB
Main genome contig sequence total:   1.1 MB (->  0.0% gap)
Main genome scaffold N/L50: 29/9.8 KB
Main genome contig N/L50:   29/9.8 KB
Number of scaffolds > 50 KB: 1
% main genome in scaffolds > 50 KB:  5.2%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       272        272    1,093,484    1,093,484   100.00%
   1 kb       172        172    1,038,642    1,038,642   100.00%
 2.5 kb       108        108      934,481      934,481   100.00%
   5 kb        58         58      760,609      760,609   100.00%
  10 kb        27         27      535,199      535,199   100.00%
  25 kb         6          6      207,060      207,060   100.00%
  50 kb         1          1       57,218       57,218   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: 31.50 +/- 4.09%

Largest Contig: 98.3 KB

Main genome scaffold total: 57
Main genome contig total:   57
Main genome scaffold sequence total: 1.0 MB
Main genome contig sequence total:   1.0 MB (->  0.0% gap)
Main genome scaffold N/L50: 8/34.1 KB
Main genome contig N/L50:   8/34.1 KB
Number of scaffolds > 50 KB: 6
% main genome in scaffolds > 50 KB: 45.4%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All        57         57    1,009,252    1,009,252   100.00%
   1 kb        57         57    1,009,252    1,009,252   100.00%
 2.5 kb        51         51      995,316      995,316   100.00%
   5 kb        34         34      938,217      938,217   100.00%
  10 kb        25         25      864,886      864,886   100.00%
  25 kb        12         12      636,043      636,043   100.00%
  50 kb         6          6      458,299      458,299   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 14:09:47 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).


								

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.