Seq. Project name:
Pseudomonas sp. JGI 0001012-A11
( Project ID: 1014783 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
Rhizosphere Grand Challenge Single Cell Sequencing
(Proposal ID: 939)
Project PI:
User Program:
Grand Challenge
Program Year:
2011
Scientific Program:
Microbial
Release Date:
2023-02-25
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Pseudomonas / Pseudomonas sp. JGI 0001012-A11 / JGI 0001012-A11 / |
| GOLD ID: | Gp0032360 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Scott Clingenpeel <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1014783
Pseudomonas sp. JGI 001012-A11
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
HAOZ 26586700 2x150 Illumina Std PE (cassava 1.8) 6600.1.48793.GTTTCG.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: 26586700 (100%)
Num contam reads removed: 1302 (0.0%)
- human_chr4 643 0.00%
- human_chr9 4 0.00%
- human_chr10 2 0.00%
- human_chr2 1 0.00%
- human_chr6 1 0.00%
Artifact reads removed: 2 (0.0%)
Normalized reads removed: 26512950 (99.7%)
Total reads removed: 26514254 (99.7%)
Total reads remaining: 72446 (0.3%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 26586700 (100%)
Num contam reads identified: 150768 (0.6%)
- Pseudomonas 129874 0.49%
- Escherichia 17832 0.07%
- Ralstonia 2462 0.01%
- Shigella 598 0.00%
- Delftia 2 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 55.45 +/- 7.27%
Largest Contig: 21.7 KB
Main genome scaffold total: 229
Main genome contig total: 229
Main genome scaffold sequence total: 331.9 KB
Main genome contig sequence total: 331.9 KB (-> 0.0% gap)
Main genome scaffold N/L50: 27/2.9 KB
Main genome contig N/L50: 27/2.9 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 229 229 331,869 331,869 100.00%
1 kb 79 79 256,694 256,694 100.00%
2.5 kb 32 32 182,573 182,573 100.00%
5 kb 15 15 123,162 123,162 100.00%
10 kb 2 2 39,646 39,646 100.00%
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: 56.08 +/- 5.24%
Largest Contig: 41.8 KB
Main genome scaffold total: 38
Main genome contig total: 38
Main genome scaffold sequence total: 235.0 KB
Main genome contig sequence total: 235.0 KB (-> 0.0% gap)
Main genome scaffold N/L50: 9/8.1 KB
Main genome contig N/L50: 9/8.1 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 38 38 235,002 235,002 100.00%
1 kb 38 38 235,002 235,002 100.00%
2.5 kb 31 31 222,676 222,676 100.00%
5 kb 18 18 177,847 177,847 100.00%
10 kb 6 6 99,748 99,748 100.00%
25 kb 1 1 41,778 41,778 100.00%
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,,,1000,100,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:
02/10/2013
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. | |
| Groups |
|---|
| ## | Name | Type |
|---|---|---|
| 1 | Gammaproteobacteria | |
| 2 | Proteobacteria |
