Seq. Project name:
Bradyrhizobium japonicum in8p8
( Project ID: 1015899 )
Product:
Microbial Minimal Draft, Isolate
Proposal Name:
Iron redox cycling genomes from the Hanford subsurface
(Proposal ID: 1137)
Project PI:
User Program:
CSP
Program Year:
2012
Scientific Program:
Microbial
Release Date:
2013-05-31
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Bradyrhizobium / Bradyrhizobium japonicum / in8p8 / |
| GOLD ID: | Gp0033198 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Eric Roden <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1015899
Bradyrhizobium japonicum
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 18561946 2x150 Illumina Std PE (cassava 1.8) 6779.1.54420.GTCCGC.fastq
2) ILLUMINA STD PE READ FILTERING STATS:
Reads were screened against synthetic oligos used in the Illumina
sequencing process. Pairs of matching reads were removed from the
dataset.
Total input reads: 18561946 (100%)
Artifact reads removed: 578980 (3.1%)
Total reads removed: 578980 (3.1%)
Total reads remaining: 17982966 (96.9%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 18561946 (100%)
Num contam reads identified: 52 (0.0%)
- Pseudomonas 26 0.00%
- Ralstonia 18 0.00%
- Delftia 4 0.00%
- Shigella 4 0.00%
4) ASSEMBLY STATS:
a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer.
Avg GC Content: 62.89 +/- 2.56%
Largest Contig: 1112.5 KB
Main genome scaffold total: 68
Main genome contig total: 78
Main genome scaffold sequence total: 7.6 MB
Main genome contig sequence total: 7.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/377.7 KB
Main genome contig N/L50: 7/342.6 KB
Number of scaffolds > 50 KB: 27
% main genome in scaffolds > 50 KB: 95.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 68 78 7,571,398 7,570,071 99.98%
1 kb 63 73 7,567,442 7,566,115 99.98%
2.5 kb 49 58 7,547,841 7,546,638 99.98%
5 kb 42 51 7,524,567 7,523,364 99.98%
10 kb 36 45 7,478,795 7,477,592 99.98%
25 kb 32 39 7,420,697 7,419,780 99.99%
50 kb 27 33 7,195,371 7,194,506 99.99%
100 kb 17 23 6,458,293 6,457,470 99.99%
250 kb 11 14 5,472,130 5,471,729 99.99%
500 kb 3 3 2,568,643 2,568,587 100.00%
1 mb 1 1 1,112,528 1,112,518 100.00%
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 artifacts.
Avg GC Content: 62.84 +/- 2.08%
Largest Contig: 1115.7 KB
Main genome scaffold total: 52
Main genome contig total: 52
Main genome scaffold sequence total: 7.6 MB
Main genome contig sequence total: 7.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/378.3 KB
Main genome contig N/L50: 7/378.3 KB
Number of scaffolds > 50 KB: 27
% main genome in scaffolds > 50 KB: 95.3%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 52 52 7,589,915 7,589,900 100.00%
1 kb 52 52 7,589,915 7,589,900 100.00%
2.5 kb 45 45 7,578,670 7,578,655 100.00%
5 kb 42 42 7,568,989 7,568,974 100.00%
10 kb 36 36 7,523,681 7,523,666 100.00%
25 kb 32 32 7,463,327 7,463,312 100.00%
50 kb 27 27 7,235,778 7,235,763 100.00%
100 kb 17 17 6,489,521 6,489,506 100.00%
250 kb 11 11 5,497,262 5,497,262 100.00%
500 kb 3 3 2,584,018 2,584,018 100.00%
1 mb 1 1 1,115,679 1,115,679 100.00%
5) KEY PIPELINE CMDS:
a) Artifact removal step:
duk params: -k 22 -s 1 -c 1
b) 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"
c) Simulated read pairing creation step:
Wgsim version: 0.3.0
Wgsim params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0
d) 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 illumina artifacts (synthetic oligos used in the laboratory).
2. Created velvet assembly of the artifact filtered data.
3. Created simulated 1-3 kb read pairs using Velvet contigs from step 2.
4. Created allpaths assembly using Velvet simulated read pairs (step 3) and the artifact filtered data.
7) ASSEMBLERS USED:
Velvet, AllpathsLG
8) RELEASE DATE:
Mon Apr 22 15:01:28 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. | |
| Groups |
|---|
| ## | Name | Type |
|---|---|---|
| 1 | Alphaproteobacteria | |
| 2 | Proteobacteria |
