Info - Euryarchaeota archaeum SCGC AAA287-N16

Seq. Project name:

Euryarchaeota archaeum SCGC AAA287-N16 ( Project ID: 1014089 )

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 1014088; SP 1014089; AP 1092680

Release Date:

2017-12-13

Organism
Genus/species/strain/isolate:	Euryarchaeota archaeon SCGC AAA287-N16 / SCGC AAA287-N16 / SCGC AAA287-N16
GOLD ID:	Gp0034072

Data Submission

NCBI BioProject ID:	190801
NCBI Tax ID:	33867
SRA accession:	SRP025077 (2013-06-11)

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

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1014089 unclassified Euryarchaeota (miscellaneous) 1) RAW DATA: LibraryName NumReads ReadType ReadType FileName NOZW 29229546 2x150 Illumina Std PE (cassava 1.8) 6668.1.51104.ATGAGC.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: 29229546 (100%) Num contam reads removed: 30 (0.0%) - human_chr2 4 0.00% - human_chr17 2 0.00% - human_chr5 2 0.00% - human_chr6 2 0.00% - human_chr13 1 0.00% - human_chr1 1 0.00% - human_chr22 1 0.00% - human_chr14 1 0.00% - human_chr3 1 0.00% Artifact reads removed: 8 (0.0%) Normalized reads removed: 29139816 (99.7%) Total reads removed: 29139854 (99.7%) Total reads remaining: 89692 (0.3%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 29229546 (100%) Num contam reads identified: 0 (0.0%) 4) ASSEMBLY STATS: a) IDBA-UD: Avg GC Content: 35.48 +/- 5.17% Largest Contig: 16.4 KB Main genome scaffold total: 235 Main genome contig total: 235 Main genome scaffold sequence total: 491.9 KB Main genome contig sequence total: 491.9 KB (-> 0.0% gap) Main genome scaffold N/L50: 33/4.0 KB Main genome contig N/L50: 33/4.0 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 235 235 491,936 491,936 100.00% 1 kb 122 122 435,867 435,867 100.00% 2.5 kb 60 60 333,597 333,597 100.00% 5 kb 23 23 204,484 204,484 100.00% 10 kb 7 7 85,745 85,745 100.00% 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: 34.46 +/- 3.40% Largest Contig: 29.7 KB Main genome scaffold total: 53 Main genome contig total: 53 Main genome scaffold sequence total: 394.9 KB Main genome contig sequence total: 394.9 KB (-> 0.0% gap) Main genome scaffold N/L50: 12/12.0 KB Main genome contig N/L50: 12/12.0 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 53 53 394,893 394,893 100.00% 1 kb 53 53 394,893 394,893 100.00% 2.5 kb 42 42 371,197 371,197 100.00% 5 kb 24 24 312,234 312,234 100.00% 10 kb 17 17 259,414 259,414 100.00% 25 kb 2 2 55,039 55,039 100.00% 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: 02/22/2013 9) AUTHORS: For additional information, please contact: NAME_OF_ANALYST - [email protected] 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 - 
1014089
unclassified Euryarchaeota (miscellaneous)

1) RAW DATA:

LibraryName	NumReads	ReadType	ReadType	FileName
NOZW	29229546	2x150	Illumina Std PE (cassava 1.8)	6668.1.51104.ATGAGC.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:          29229546 (100%)
Num contam reads removed:   30 (0.0%)
  - human_chr2 	4	0.00%
  - human_chr17	2	0.00%
  - human_chr5 	2	0.00%
  - human_chr6 	2	0.00%
  - human_chr13	1	0.00%
  - human_chr1 	1	0.00%
  - human_chr22	1	0.00%
  - human_chr14	1	0.00%
  - human_chr3 	1	0.00%
Artifact reads removed:     8 (0.0%)
Normalized reads removed:   29139816 (99.7%)
Total reads removed:        29139854 (99.7%)
Total reads remaining:      89692 (0.3%)

3) ILLUMINA STD PE READ IDENTIFICATION STATS

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

Total input reads:           29229546 (100%)
Num contam reads identified: 0 (0.0%)

4) ASSEMBLY STATS:

a) IDBA-UD:
Avg GC Content: 35.48 +/- 5.17%

Largest Contig: 16.4 KB

Main genome scaffold total: 235
Main genome contig total:   235
Main genome scaffold sequence total: 491.9 KB
Main genome contig sequence total:   491.9 KB (->  0.0% gap)
Main genome scaffold N/L50: 33/4.0 KB
Main genome contig N/L50:   33/4.0 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       235        235      491,936      491,936   100.00%
   1 kb       122        122      435,867      435,867   100.00%
 2.5 kb        60         60      333,597      333,597   100.00%
   5 kb        23         23      204,484      204,484   100.00%
  10 kb         7          7       85,745       85,745   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: 34.46 +/- 3.40%

Largest Contig: 29.7 KB

Main genome scaffold total: 53
Main genome contig total:   53
Main genome scaffold sequence total: 394.9 KB
Main genome contig sequence total:   394.9 KB (->  0.0% gap)
Main genome scaffold N/L50: 12/12.0 KB
Main genome contig N/L50:   12/12.0 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        53         53      394,893      394,893   100.00%
   1 kb        53         53      394,893      394,893   100.00%
 2.5 kb        42         42      371,197      371,197   100.00%
   5 kb        24         24      312,234      312,234   100.00%
  10 kb        17         17      259,414      259,414   100.00%
  25 kb         2          2       55,039       55,039   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:
02/22/2013

9) AUTHORS:
For additional information, please contact:
NAME_OF_ANALYST - [email protected]
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.