Info - Thaumarchaeota archaeon SCGC AB-663-O07

Seq. Project name:

Thaumarchaeota archaeon SCGC AB-663-O07 ( Project ID: 1014176 )

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 1014175; SP 1014176; AP 1066673; AP 1014177

Release Date:

2017-12-13

Organism
Genus/species/strain/isolate:	Thaumarchaeota archaeon SCGC AB-663-O07 / SCGC AB-663-O07 / SCGC AB-663-O07
GOLD ID:	Gp0033650

Data Submission

NCBI BioProject ID:	195685
NCBI Tax ID:	1313312
SRA accession:	SRP024946 (2013-06-10)

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

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1014176 unclassified Thaumarchaeota (miscellaneous) 1) RAW DATA: LibraryName NumReads ReadType ReadType FileName NPBA 20595744 2x157 Illumina Std PE (cassava 1.8) 6669.3.51255.TCGAAG.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: 20595744 (100%) Num contam reads removed: 2 (0.0%) - human_chr7 1 0.00% Artifact reads removed: 2 (0.0%) Normalized reads removed: 20483662 (99.5%) Total reads removed: 20483666 (99.5%) Total reads remaining: 112078 (0.5%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 20595744 (100%) Num contam reads identified: 8 (0.0%) - Delftia 8 0.00% 4) ASSEMBLY STATS: a) IDBA-UD: Avg GC Content: 33.78 +/- 4.56% Largest Contig: 38.7 KB Main genome scaffold total: 225 Main genome contig total: 225 Main genome scaffold sequence total: 586.4 KB Main genome contig sequence total: 586.4 KB (-> 0.0% gap) Main genome scaffold N/L50: 24/6.2 KB Main genome contig N/L50: 24/6.2 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 225 225 586,356 586,356 100.00% 1 kb 117 117 528,832 528,832 100.00% 2.5 kb 61 61 440,157 440,157 100.00% 5 kb 30 30 331,252 331,252 100.00% 10 kb 14 14 216,666 216,666 100.00% 25 kb 1 1 38,671 38,671 100.00% 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: 32.99 +/- 1.86% Largest Contig: 69.9 KB Main genome scaffold total: 37 Main genome contig total: 37 Main genome scaffold sequence total: 477.2 KB Main genome contig sequence total: 477.2 KB (-> 0.0% gap) Main genome scaffold N/L50: 6/21.9 KB Main genome contig N/L50: 6/21.9 KB Number of scaffolds > 50 KB: 3 % main genome in scaffolds > 50 KB: 38.6% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 37 37 477,190 477,190 100.00% 1 kb 37 37 477,190 477,190 100.00% 2.5 kb 32 32 466,044 466,044 100.00% 5 kb 20 20 426,417 426,417 100.00% 10 kb 15 15 386,344 386,344 100.00% 25 kb 4 4 214,445 214,445 100.00% 50 kb 3 3 184,303 184,303 100.00% 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: Mon Apr 8 14:23:07 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 - 
1014176
unclassified Thaumarchaeota (miscellaneous)

1) RAW DATA:

LibraryName	NumReads	ReadType	ReadType	FileName
NPBA	20595744	2x157	Illumina Std PE (cassava 1.8)	6669.3.51255.TCGAAG.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:          20595744 (100%)
Num contam reads removed:   2 (0.0%)
  - human_chr7	1	0.00%
Artifact reads removed:     2 (0.0%)
Normalized reads removed:   20483662 (99.5%)
Total reads removed:        20483666 (99.5%)
Total reads remaining:      112078 (0.5%)

3) ILLUMINA STD PE READ IDENTIFICATION STATS

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

Total input reads:           20595744 (100%)
Num contam reads identified: 8 (0.0%)
  - Delftia	8	0.00%

4) ASSEMBLY STATS:

a) IDBA-UD:
Avg GC Content: 33.78 +/- 4.56%

Largest Contig: 38.7 KB

Main genome scaffold total: 225
Main genome contig total:   225
Main genome scaffold sequence total: 586.4 KB
Main genome contig sequence total:   586.4 KB (->  0.0% gap)
Main genome scaffold N/L50: 24/6.2 KB
Main genome contig N/L50:   24/6.2 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       225        225      586,356      586,356   100.00%
   1 kb       117        117      528,832      528,832   100.00%
 2.5 kb        61         61      440,157      440,157   100.00%
   5 kb        30         30      331,252      331,252   100.00%
  10 kb        14         14      216,666      216,666   100.00%
  25 kb         1          1       38,671       38,671   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: 32.99 +/- 1.86%

Largest Contig: 69.9 KB

Main genome scaffold total: 37
Main genome contig total:   37
Main genome scaffold sequence total: 477.2 KB
Main genome contig sequence total:   477.2 KB (->  0.0% gap)
Main genome scaffold N/L50: 6/21.9 KB
Main genome contig N/L50:   6/21.9 KB
Number of scaffolds > 50 KB: 3
% main genome in scaffolds > 50 KB: 38.6%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All        37         37      477,190      477,190   100.00%
   1 kb        37         37      477,190      477,190   100.00%
 2.5 kb        32         32      466,044      466,044   100.00%
   5 kb        20         20      426,417      426,417   100.00%
  10 kb        15         15      386,344      386,344   100.00%
  25 kb         4          4      214,445      214,445   100.00%
  50 kb         3          3      184,303      184,303   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:
Mon Apr  8 14:23:07 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.

Groups

This portal belongs to the following groups

##	Name	Type
1	Thaumarchaeota