Seq. Project name:
Bradyrhizobium japonicum is5
( Project ID: 1015902 )
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 / is5 / |
| GOLD ID: | Gp0033199 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Eric Roden <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1015902
Bradyrhizobium japonicum
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 21607350 2x150 Illumina Std PE (cassava 1.8) 6779.1.54420.GTGAAA.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: 21607350 (100%)
Artifact reads removed: 1025564 (4.7%)
Total reads removed: 1025564 (4.7%)
Total reads remaining: 20581786 (95.3%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 21607350 (100%)
Num contam reads identified: 106 (0.0%)
- Ralstonia 46 0.00%
- Delftia 22 0.00%
- Cupriavidus 20 0.00%
- Pseudomonas 16 0.00%
- Escherichia 2 0.00%
4) ASSEMBLY STATS:
a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer.
Avg GC Content: 62.68 +/- 2.57%
Largest Contig: 1128.9 KB
Main genome scaffold total: 79
Main genome contig total: 86
Main genome scaffold sequence total: 7.6 MB
Main genome contig sequence total: 7.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/377.8 KB
Main genome contig N/L50: 8/330.9 KB
Number of scaffolds > 50 KB: 29
% main genome in scaffolds > 50 KB: 92.6%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 79 86 7,570,804 7,569,988 99.99%
1 kb 73 80 7,566,883 7,566,067 99.99%
2.5 kb 56 62 7,542,542 7,541,871 99.99%
5 kb 50 56 7,522,176 7,521,517 99.99%
10 kb 42 48 7,462,470 7,461,821 99.99%
25 kb 38 44 7,398,839 7,398,200 99.99%
50 kb 29 35 7,007,885 7,007,246 99.99%
100 kb 16 22 5,994,225 5,993,596 99.99%
250 kb 11 16 5,186,198 5,185,694 99.99%
500 kb 2 3 1,870,750 1,870,642 99.99%
1 mb 1 2 1,128,901 1,128,803 99.99%
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: 62.60 +/- 2.07%
Largest Contig: 1129.4 KB
Main genome scaffold total: 60
Main genome contig total: 60
Main genome scaffold sequence total: 7.6 MB
Main genome contig sequence total: 7.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/378.2 KB
Main genome contig N/L50: 7/378.2 KB
Number of scaffolds > 50 KB: 28
% main genome in scaffolds > 50 KB: 93.2%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 60 60 7,588,794 7,588,794 100.00%
1 kb 60 60 7,588,794 7,588,794 100.00%
2.5 kb 52 52 7,576,142 7,576,142 100.00%
5 kb 49 49 7,564,761 7,564,761 100.00%
10 kb 39 39 7,484,115 7,484,115 100.00%
25 kb 36 36 7,428,746 7,428,746 100.00%
50 kb 28 28 7,069,285 7,069,285 100.00%
100 kb 16 16 6,105,621 6,105,621 100.00%
250 kb 11 11 5,294,216 5,294,216 100.00%
500 kb 3 3 2,387,268 2,387,268 100.00%
1 mb 1 1 1,129,416 1,129,416 100.00%
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 14:55:35 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 |
