Info - Euryarchaeota archaeon SCGC AB-629-J07

Seq. Project name:

Euryarchaeota archaeon SCGC AB-629-J07 ( Project ID: 1014095 )

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 1014094; SP 1014095; AP 1014096; AP 1066653

Release Date:

2023-02-24

Organism
Genus/species/strain/isolate:	Euryarchaeota archaeon SCGC AB-629-J07 / SCGC AB-629-J07 / SCGC AB-629-J07
GOLD ID:	Gp0033952

Data Submission

NCBI BioProject ID:	190800
NCBI Tax ID:	1298893
SRA accession:	SRP024941 (2013-06-10)

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

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1014095 unclassified Euryarchaeota (miscellaneous) 1) RAW DATA: LibraryName NumReads ReadType ReadType FileName NPAW 30815702 2x157 Illumina Std PE (cassava 1.8) 6669.1.51253.CACTCA.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: 30815702 (100%) Num contam reads removed: 2 (0.0%) - human_chr9 1 0.00% Artifact reads removed: 722 (0.0%) Normalized reads removed: 30501514 (99.0%) Total reads removed: 30502238 (99.0%) Total reads remaining: 313464 (1.0%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 30815702 (100%) Num contam reads identified: 0 (0.0%) 4) ASSEMBLY STATS: a) IDBA-UD: Avg GC Content: 35.70 +/- 5.48% Largest Contig: 45.8 KB Main genome scaffold total: 450 Main genome contig total: 450 Main genome scaffold sequence total: 1.5 MB Main genome contig sequence total: 1.5 MB (-> 0.0% gap) Main genome scaffold N/L50: 46/8.3 KB Main genome contig N/L50: 46/8.3 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 450 450 1,467,439 1,467,439 100.00% 1 kb 237 237 1,360,185 1,360,185 100.00% 2.5 kb 147 147 1,215,965 1,215,965 100.00% 5 kb 86 86 996,340 996,340 100.00% 10 kb 33 33 621,997 621,997 100.00% 25 kb 7 7 244,673 244,673 100.00% 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: 35.47 +/- 4.04% Largest Contig: 75.6 KB Main genome scaffold total: 100 Main genome contig total: 102 Main genome scaffold sequence total: 1.3 MB Main genome contig sequence total: 1.3 MB (-> 0.3% gap) Main genome scaffold N/L50: 15/21.4 KB Main genome contig N/L50: 15/21.4 KB Number of scaffolds > 50 KB: 5 % main genome in scaffolds > 50 KB: 25.0% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 100 102 1,298,995 1,295,214 99.71% 1 kb 100 102 1,298,995 1,295,214 99.71% 2.5 kb 84 86 1,262,827 1,259,046 99.70% 5 kb 66 68 1,199,250 1,195,469 99.68% 10 kb 41 43 1,020,709 1,016,928 99.63% 25 kb 12 12 589,442 589,442 100.00% 50 kb 5 5 325,055 325,055 100.00% 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: Thu Apr 4 10:39:51 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 - 
1014095
unclassified Euryarchaeota (miscellaneous)

1) RAW DATA:

LibraryName	NumReads	ReadType	ReadType	FileName
NPAW	30815702	2x157	Illumina Std PE (cassava 1.8)	6669.1.51253.CACTCA.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:          30815702 (100%)
Num contam reads removed:   2 (0.0%)
  - human_chr9	1	0.00%
Artifact reads removed:     722 (0.0%)
Normalized reads removed:   30501514 (99.0%)
Total reads removed:        30502238 (99.0%)
Total reads remaining:      313464 (1.0%)

3) ILLUMINA STD PE READ IDENTIFICATION STATS

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

Total input reads:           30815702 (100%)
Num contam reads identified: 0 (0.0%)

4) ASSEMBLY STATS:

a) IDBA-UD:
Avg GC Content: 35.70 +/- 5.48%

Largest Contig: 45.8 KB

Main genome scaffold total: 450
Main genome contig total:   450
Main genome scaffold sequence total: 1.5 MB
Main genome contig sequence total:   1.5 MB (->  0.0% gap)
Main genome scaffold N/L50: 46/8.3 KB
Main genome contig N/L50:   46/8.3 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       450        450    1,467,439    1,467,439   100.00%
   1 kb       237        237    1,360,185    1,360,185   100.00%
 2.5 kb       147        147    1,215,965    1,215,965   100.00%
   5 kb        86         86      996,340      996,340   100.00%
  10 kb        33         33      621,997      621,997   100.00%
  25 kb         7          7      244,673      244,673   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: 35.47 +/- 4.04%

Largest Contig: 75.6 KB

Main genome scaffold total: 100
Main genome contig total:   102
Main genome scaffold sequence total: 1.3 MB
Main genome contig sequence total:   1.3 MB (->  0.3% gap)
Main genome scaffold N/L50: 15/21.4 KB
Main genome contig N/L50:   15/21.4 KB
Number of scaffolds > 50 KB: 5
% main genome in scaffolds > 50 KB: 25.0%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       100        102    1,298,995    1,295,214    99.71%
   1 kb       100        102    1,298,995    1,295,214    99.71%
 2.5 kb        84         86    1,262,827    1,259,046    99.70%
   5 kb        66         68    1,199,250    1,195,469    99.68%
  10 kb        41         43    1,020,709    1,016,928    99.63%
  25 kb        12         12      589,442      589,442   100.00%
  50 kb         5          5      325,055      325,055   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:
Thu Apr  4 10:39:51 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.