Info - Euryarchaeota archaeon SCGC AB-633-I06

Seq. Project name:

Euryarchaeota archaeon SCGC AB-633-I06 ( Project ID: 1014098 )

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 1014097; SP 1014098; AP 1092681

Release Date:

2017-12-13

Organism
Genus/species/strain/isolate:	archaeon SCGC AB-633-I06 / SCGC AB-633-I06 / SCGC AB-633-I06
GOLD ID:	Gp0034076

Data Submission

NCBI BioProject ID:	190809
NCBI Tax ID:	1298897
SRA accession:	SRP024945 (2013-06-10)

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

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1014098 unclassified Euryarchaeota (miscellaneous) 1) RAW DATA: LibraryName NumReads ReadType ReadType FileName LIB 32076660 2x157 Illumina Std PE (cassava 1.8) 6669.1.51253.CATGGC.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: 32076660 (100%) Num contam reads removed: 2 (0.0%) - human_chr18 1 0.00% Artifact reads removed: 145318 (0.5%) Normalized reads removed: 31850372 (99.3%) Total reads removed: 31995692 (99.7%) Total reads remaining: 80968 (0.3%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 32076660 (100%) Num contam reads identified: 4 (0.0%) - Escherichia 2 0.00% - Shigella 2 0.00% 4) ASSEMBLY STATS: a) IDBA-UD: Avg GC Content: 36.95 +/- 7.34% Largest Contig: 17.7 KB Main genome scaffold total: 203 Main genome contig total: 203 Main genome scaffold sequence total: 398.0 KB Main genome contig sequence total: 398.0 KB (-> 0.0% gap) Main genome scaffold N/L50: 21/5.2 KB Main genome contig N/L50: 21/5.2 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 203 203 398,011 398,011 100.00% 1 kb 78 78 335,855 335,855 100.00% 2.5 kb 41 41 274,468 274,468 100.00% 5 kb 22 22 204,878 204,878 100.00% 10 kb 8 8 115,189 115,189 100.00% 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: 37.10 +/- 5.12% Largest Contig: 37.8 KB Main genome scaffold total: 34 Main genome contig total: 34 Main genome scaffold sequence total: 316.7 KB Main genome contig sequence total: 316.7 KB (-> 0.0% gap) Main genome scaffold N/L50: 7/14.3 KB Main genome contig N/L50: 7/14.3 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 34 34 316,733 316,723 100.00% 1 kb 34 34 316,733 316,723 100.00% 2.5 kb 29 29 306,022 306,012 100.00% 5 kb 21 21 277,784 277,774 100.00% 10 kb 10 10 196,583 196,573 99.99% 25 kb 3 3 101,146 101,146 100.00% 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: Tue Apr 9 09:33:57 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 - 
1014098
unclassified Euryarchaeota (miscellaneous)

1) RAW DATA:

LibraryName	NumReads	ReadType	ReadType	FileName
LIB	32076660	2x157	Illumina Std PE (cassava 1.8)	6669.1.51253.CATGGC.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:          32076660 (100%)
Num contam reads removed:   2 (0.0%)
  - human_chr18	1	0.00%
Artifact reads removed:     145318 (0.5%)
Normalized reads removed:   31850372 (99.3%)
Total reads removed:        31995692 (99.7%)
Total reads remaining:      80968 (0.3%)

3) ILLUMINA STD PE READ IDENTIFICATION STATS

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

Total input reads:           32076660 (100%)
Num contam reads identified: 4 (0.0%)
  - Escherichia	2	0.00%
  - Shigella   	2	0.00%

4) ASSEMBLY STATS:

a) IDBA-UD:
Avg GC Content: 36.95 +/- 7.34%

Largest Contig: 17.7 KB

Main genome scaffold total: 203
Main genome contig total:   203
Main genome scaffold sequence total: 398.0 KB
Main genome contig sequence total:   398.0 KB (->  0.0% gap)
Main genome scaffold N/L50: 21/5.2 KB
Main genome contig N/L50:   21/5.2 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       203        203      398,011      398,011   100.00%
   1 kb        78         78      335,855      335,855   100.00%
 2.5 kb        41         41      274,468      274,468   100.00%
   5 kb        22         22      204,878      204,878   100.00%
  10 kb         8          8      115,189      115,189   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: 37.10 +/- 5.12%

Largest Contig: 37.8 KB

Main genome scaffold total: 34
Main genome contig total:   34
Main genome scaffold sequence total: 316.7 KB
Main genome contig sequence total:   316.7 KB (->  0.0% gap)
Main genome scaffold N/L50: 7/14.3 KB
Main genome contig N/L50:   7/14.3 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        34         34      316,733      316,723   100.00%
   1 kb        34         34      316,733      316,723   100.00%
 2.5 kb        29         29      306,022      306,012   100.00%
   5 kb        21         21      277,784      277,774   100.00%
  10 kb        10         10      196,583      196,573    99.99%
  25 kb         3          3      101,146      101,146   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:
Tue Apr  9 09:33:57 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.