Info - Crenarchaeota archaeon SCGC AAA261-F05

Seq. Project name:

Crenarchaeota archaeon SCGC AAA261-F05 ( Project ID: 405175 )

Product:

Standard Draft

Proposal Name:

Single Cells Yellowstone National Park - OSP_D (Iron oxidizer mat) (Proposal ID: 934)

Project PI:

William Inskeep

User Program:

GEBA

Program Year:

2011

Scientific Program:

Microbial

Genome Portal:

2264867023

Related Projects:

FD 1079622; SP 405175; AP 1423611

Release Date:

2012-07-11

Organism
Genus/species/strain/isolate:	Crenarchaeota archaeon SCGC AAA261-F05 / SCGC AAA261-F05 /
GOLD ID:	Gp0015559

Data Submission

NCBI BioProject ID:	165471
NCBI Tax ID:	1130300
SRA accession:	SRP079409 (2016-07-23)

Contacts
JGI:	[email protected]
Request DNA:	William Inskeep <[email protected]>

General Information
	QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 4096626 crenarchaeote SCGC AAA261-F05 1) RAW DATA: LibraryName NumReads ReadType FileName INXW 41019594 2x150 2259.3.1848.CAAAAG.fastq 2) STD 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: 41019594 (100%) Num contam reads removed: 52 (0.0%) - human_chr3 24 0.00% - human_chr2 8 0.00% - human_chrX 6 0.00% - human_chr1 2 0.00% - human_chr14 2 0.00% - human_chr10 2 0.00% - human_chr7 2 0.00% - human_chr9 2 0.00% - human_chr6 2 0.00% - human_chr15 2 0.00% Artifact reads removed: 252144 (0.6%) Normalized reads removed: 40600336 (99.0%) Total reads removed: 40852532 (99.6%) Total reads remaining: 167062 (0.4%) 3) STD READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 41019594 (100%) Num contam reads identified: 14 (0.0%) - Delftia 8 0.00% - Escherichia 4 0.00% - Shigella 2 0.00% 4) ASSEMBLY STATS: a) Velvet assembly using VelvetOptimizer: Assembly stats of the Velvet assembly created by the velvet optimizer. The input reads have been filtered for contamination, artifacts and normalized. Avg GC Content: 33.11 +/- 5.13% Largest Contig: 69.3 KB Main genome scaffold total: 179 Main genome contig total: 190 Main genome scaffold sequence total: 714.8 KB Main genome contig sequence total: 712.0 KB (-> 0.1% gap) Main genome scaffold N/L50: 17/9.8 KB Main genome contig N/L50: 18/9.5 KB Number of scaffolds > 50 KB: 2 % main genome in scaffolds > 50 KB: 17.1% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 179 190 714,798 711,992 99.61% 1 kb 96 104 657,401 655,059 99.64% 2.5 kb 59 65 599,218 597,226 99.67% 5 kb 42 48 539,426 537,674 99.68% 10 kb 16 19 351,611 350,613 99.72% 25 kb 3 4 163,344 163,023 99.80% 50 kb 2 2 122,428 122,268 99.87% b) Allpaths + Velvet simulated read pairs: Assembly stats of the ALLPATHS assembly. The input contains simulated 1-3 kb read pairs created from the Velvet assembly and reads that have been filtered for contamination, artifacts and normalized. Avg GC Content: 32.70 +/- 3.46% Largest Contig: 52.7 KB Main genome scaffold total: 105 Main genome contig total: 105 Main genome scaffold sequence total: 672.9 KB Main genome contig sequence total: 672.9 KB (-> 0.0% gap) Main genome scaffold N/L50: 18/9.9 KB Main genome contig N/L50: 18/9.9 KB Number of scaffolds > 50 KB: 2 % main genome in scaffolds > 50 KB: 15.3% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 105 105 672,934 672,934 100.00% 1 kb 103 103 671,386 671,386 100.00% 2.5 kb 65 65 612,745 612,745 100.00% 5 kb 49 49 555,957 555,957 100.00% 10 kb 16 16 320,829 320,829 100.00% 25 kb 3 3 143,630 143,630 100.00% 50 kb 2 2 102,942 102,942 100.00% c) Merged Allpaths and optimized Velvet assemblies: Assembly stats of the final assembly. This assembly was performed using a hybrid of the ALLPATHS (referenced above) and Velvet optimized assemblies. The Velvet optimized assemblies were performed using reads that have been filtered for contamination, artifact and normalized. These assemblies were chosen based on the best kmer based on largest contig lengths and varying coverage cutoffs. The contigs of the velvet assemblies and the ALLPATHS assembly were merged and unique sequences selected. Avg GC Content: 33.25 +/- 5.01% Largest Contig: 53.2 KB Main genome scaffold total: 179 Main genome contig total: 179 Main genome scaffold sequence total: 716.0 KB Main genome contig sequence total: 716.0 KB (-> 0.0% gap) Main genome scaffold N/L50: 21/9.1 KB Main genome contig N/L50: 21/9.1 KB Number of scaffolds > 50 KB: 2 % main genome in scaffolds > 50 KB: 14.4% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 179 179 716,004 716,004 100.00% 1 kb 107 107 666,867 666,867 100.00% 2.5 kb 66 66 602,137 602,137 100.00% 5 kb 47 47 536,724 536,724 100.00% 10 kb 18 18 336,859 336,859 100.00% 25 kb 3 3 144,109 144,109 100.00% 50 kb 2 2 103,421 103,421 100.00% 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) Velvet assembly step for creating simulated read pairs: Velvet version: 1.1.04 Velvet optimizer version: 2.1.7 Velvet optimizer params: --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500" e) Simulated read pairing creation step: Wgsim version: 0.3.0 Wgsim params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0 f) ALLPATHS assembly step: ALLPATHS version: r41043 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,1,200,35,,,inward,0,0 SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0 g) Velvet assembly step (varying kmer and coverage cutoffs): Velvet version: 1.1.04 Best Kmer: 43 Best cutoff coverages: 1 5 10 auto 6) WORKFLOW STEPS: 1. Removed contamination (human contaminants). 2. Removed illumina artifacts (synthetic oligos used in the laboratory). 3. Normalized read coverage. 4. Created velvet assembly of the contam+artifact+normalized filtered data. 5. Created simulated 1-3 kb read pairs using velvet contigs from step 4. 6. Created allpaths assembly using velvet simulated read pairs (step 5) and the contam+artifact+normalized filtered data. 7. Ran multiple velvet assemblies at different kmer and coverage windows using the contam+artifact+normalized filtered data. Merged velvet contigs with allpaths contigs from step 6 and select only unique sequences. 7) RELEASE DATE: Mon May 14 09:50:29 PDT 2012 By Alexander Spunde- [email protected] 8) AUTHORS: For additional information, please contact: Stephan Trong - [email protected] James Han - [email protected] 9) ADDITIONAL COMMENTS: Run base output HIGH. Read quality HIGH. Target genome is present in BLAST hits. Assembly nucleotide coverage is 80x using 1 lane(s) of data Y evidence of process contamination: acceptable for Single Cell. NOTE: hits for Crenarchaeota (target) in 16S, Methanospirillum (contam) in NT. This file was automatically generated by the jigsaw pipeline software (version 2.0.1).

General Information

QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 
4096626
crenarchaeote SCGC AAA261-F05

1) RAW DATA:

LibraryName	NumReads	ReadType	FileName
INXW	41019594	2x150	2259.3.1848.CAAAAG.fastq


2) STD 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:          41019594 (100%)
Num contam reads removed:   52 (0.0%)
  - human_chr3 	24	0.00%
  - human_chr2 	8	0.00%
  - human_chrX 	6	0.00%
  - human_chr1 	2	0.00%
  - human_chr14	2	0.00%
  - human_chr10	2	0.00%
  - human_chr7 	2	0.00%
  - human_chr9 	2	0.00%
  - human_chr6 	2	0.00%
  - human_chr15	2	0.00%
Artifact reads removed:     252144 (0.6%)
Normalized reads removed:   40600336 (99.0%)
Total reads removed:        40852532 (99.6%)
Total reads remaining:      167062 (0.4%)

3) STD READ IDENTIFICATION STATS

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

Total input reads:           41019594 (100%)
Num contam reads identified: 14 (0.0%)
  - Delftia    	8	0.00%
  - Escherichia	4	0.00%
  - Shigella   	2	0.00%

4) ASSEMBLY STATS:

a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer. The input reads have been filtered for contamination,
artifacts and normalized.

Avg GC Content: 33.11 +/- 5.13%

Largest Contig: 69.3 KB

Main genome scaffold total: 179
Main genome contig total:   190
Main genome scaffold sequence total: 714.8 KB
Main genome contig sequence total:   712.0 KB (->  0.1% gap)
Main genome scaffold N/L50: 17/9.8 KB
Main genome contig N/L50:   18/9.5 KB
Number of scaffolds > 50 KB: 2
% main genome in scaffolds > 50 KB: 17.1%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       179        190      714,798      711,992    99.61%
   1 kb        96        104      657,401      655,059    99.64%
 2.5 kb        59         65      599,218      597,226    99.67%
   5 kb        42         48      539,426      537,674    99.68%
  10 kb        16         19      351,611      350,613    99.72%
  25 kb         3          4      163,344      163,023    99.80%
  50 kb         2          2      122,428      122,268    99.87%

b) Allpaths + Velvet simulated read pairs:
Assembly stats of the ALLPATHS assembly. The input contains simulated
1-3 kb read pairs created from the Velvet assembly and reads that
have been filtered for contamination, artifacts and normalized.

Avg GC Content: 32.70 +/- 3.46%

Largest Contig: 52.7 KB

Main genome scaffold total: 105
Main genome contig total:   105
Main genome scaffold sequence total: 672.9 KB
Main genome contig sequence total:   672.9 KB (->  0.0% gap)
Main genome scaffold N/L50: 18/9.9 KB
Main genome contig N/L50:   18/9.9 KB
Number of scaffolds > 50 KB: 2
% main genome in scaffolds > 50 KB: 15.3%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       105        105      672,934      672,934   100.00%
   1 kb       103        103      671,386      671,386   100.00%
 2.5 kb        65         65      612,745      612,745   100.00%
   5 kb        49         49      555,957      555,957   100.00%
  10 kb        16         16      320,829      320,829   100.00%
  25 kb         3          3      143,630      143,630   100.00%
  50 kb         2          2      102,942      102,942   100.00%

c) Merged Allpaths and optimized Velvet assemblies:
Assembly stats of the final assembly. This assembly was performed
using a hybrid of the ALLPATHS (referenced above) and Velvet
optimized assemblies. The Velvet optimized assemblies were performed
using reads that have been filtered for contamination, artifact and
normalized. These assemblies were chosen based on the best kmer based
on largest contig lengths and varying coverage cutoffs. The contigs
of the velvet assemblies and the ALLPATHS assembly were merged and
unique sequences selected.

Avg GC Content: 33.25 +/- 5.01%

Largest Contig: 53.2 KB

Main genome scaffold total: 179
Main genome contig total:   179
Main genome scaffold sequence total: 716.0 KB
Main genome contig sequence total:   716.0 KB (->  0.0% gap)
Main genome scaffold N/L50: 21/9.1 KB
Main genome contig N/L50:   21/9.1 KB
Number of scaffolds > 50 KB: 2
% main genome in scaffolds > 50 KB: 14.4%

 Minimum    Number    Number     Total        Total     Scaffold
Scaffold      of        of      Scaffold      Contig     Contig
 Length   Scaffolds  Contigs     Length       Length    Coverage
--------  ---------  -------  -----------  -----------  --------
    All       179        179      716,004      716,004   100.00%
   1 kb       107        107      666,867      666,867   100.00%
 2.5 kb        66         66      602,137      602,137   100.00%
   5 kb        47         47      536,724      536,724   100.00%
  10 kb        18         18      336,859      336,859   100.00%
  25 kb         3          3      144,109      144,109   100.00%
  50 kb         2          2      103,421      103,421   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) Velvet assembly step for creating simulated read pairs:
Velvet version: 1.1.04
Velvet optimizer version: 2.1.7
Velvet optimizer params: --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500"

e) Simulated read pairing creation step:
Wgsim version: 0.3.0
Wgsim params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0

f) ALLPATHS assembly step:
ALLPATHS version: r41043
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,1,200,35,,,inward,0,0
SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0

g) Velvet assembly step (varying kmer and coverage cutoffs):
Velvet version: 1.1.04
Best Kmer: 43
Best cutoff coverages:
1
5
10
auto

6) WORKFLOW STEPS:
1. Removed contamination (human contaminants).
2. Removed illumina artifacts (synthetic oligos used in the laboratory).
3. Normalized read coverage.
4. Created velvet assembly of the contam+artifact+normalized filtered data.
5. Created simulated 1-3 kb read pairs using velvet contigs from step 4.
6. Created allpaths assembly using velvet simulated read pairs (step 5) and the contam+artifact+normalized filtered data.
7. Ran multiple velvet assemblies at different kmer and coverage windows using the contam+artifact+normalized filtered data. Merged velvet contigs with allpaths contigs from step 6 and select only unique sequences.

7) RELEASE DATE:
Mon May 14 09:50:29 PDT 2012 By Alexander Spunde- [email protected]

8) AUTHORS:
For additional information, please contact:
Stephan Trong - [email protected]
James Han - [email protected]

9) ADDITIONAL COMMENTS:
Run base output HIGH.
Read quality HIGH.
Target genome is present in BLAST hits.
Assembly nucleotide coverage is 80x using 1 lane(s) of data
Y evidence of process contamination: acceptable for Single Cell.
NOTE: hits for Crenarchaeota (target) in 16S, Methanospirillum (contam) in NT. 

This file was automatically generated by the jigsaw pipeline software (version 2.0.1).


								

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.

Groups

This portal belongs to the following groups

##	Name	Type
1	Crenarchaeota
2	Environmental