Seq. Project name:
Bradyrhizobium elkanii USDA 3259
( Project ID: 404532 )
Product:
Standard Draft
Proposal Name:
GEBA Root Nodulating Bacteria
(Proposal ID: 882)
Project PI:
User Program:
DD
Program Year:
2010
Scientific Program:
Microbial
Genome Portal:
Release Date:
2012-05-10
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Bradyrhizobium / Bradyrhizobium pachyrhizi / USDA 3259 / |
| GOLD ID: | Gp0009818 |
| Contacts | |
|---|---|
| JGI: | IMG [email protected] |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
4095474
Bradyhrizobium elkanii USDA 3259
1) RAW DATA:
LibraryName NumReads ReadType FileName
IGOB 21714486 2x150 2154.1.1784.ACTTGA.fastq
2) READ FILTERING STATS:
Pairs of matching reads were removed from the dataset.
Total input reads: 21714486 (100%)
Artifact reads removed: 172908 (0.8%)
Trimmed reads removed: 562948 (2.6%)
Total reads removed: 735856 (3.4%)
Total reads remaining: 20978630 (96.6%)
3) ASSEMBLY STATS:
b) Velvet assembly:
Assembly stats of the Velvet assembly created by the velvet
optimizer. The input reads have been .
Avg GC Content: 62.57 +/- 2.89%
Largest Contig: 629.0 KB
Main genome scaffold total: 149
Main genome contig total: 193
Main genome scaffold sequence total: 8.7 MB
Main genome contig sequence total: 8.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 11/248.5 KB
Main genome contig N/L50: 21/106.6 KB
Number of scaffolds > 50 KB: 41
% main genome in scaffolds > 50 KB: 85.9%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 149 193 8,714,439 8,710,431 99.95%
1 kb 129 173 8,700,239 8,696,231 99.95%
2.5 kb 109 152 8,669,641 8,665,790 99.96%
5 kb 95 138 8,615,315 8,611,464 99.96%
10 kb 86 129 8,547,932 8,544,081 99.95%
25 kb 58 101 8,089,050 8,085,199 99.95%
50 kb 41 79 7,482,605 7,479,154 99.95%
100 kb 22 55 6,073,007 6,070,046 99.95%
250 kb 10 34 4,158,607 4,156,470 99.95%
500 kb 3 11 1,761,141 1,760,427 99.96%
c) 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 .
Avg GC Content: 62.54 +/- 2.69%
Largest Contig: 629.3 KB
Main genome scaffold total: 101
Main genome contig total: 102
Main genome scaffold sequence total: 8.7 MB
Main genome contig sequence total: 8.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 11/246.0 KB
Main genome contig N/L50: 11/246.0 KB
Number of scaffolds > 50 KB: 45
% main genome in scaffolds > 50 KB: 90.7%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 101 102 8,722,461 8,722,236 100.00%
1 kb 101 102 8,722,461 8,722,236 100.00%
2.5 kb 90 91 8,704,846 8,704,621 100.00%
5 kb 84 85 8,680,495 8,680,270 100.00%
10 kb 76 77 8,621,280 8,621,055 100.00%
25 kb 55 56 8,258,964 8,258,739 100.00%
50 kb 45 46 7,912,978 7,912,753 100.00%
100 kb 25 26 6,475,475 6,475,250 100.00%
250 kb 10 10 4,164,914 4,164,914 100.00%
500 kb 3 3 1,762,644 1,762,644 100.00%
4) KEY PIPELINE CMDS:
a) 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 2 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500"
b) Simulated read pairing creation step:
Wgsim version: 0.3.0
Wgsim params: -e 0 -1 76 -2 76 -r 0 -R 0 -X 0
c) ALLPATHS assembly step:
ALLPATHS version: r39750
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
5) WORKFLOW STEPS:
1. Removed illumina artifacts (synthetic oligos used in the laboratory).
2. Created velvet assembly of the artifact filtered data (using velvet optimiser).
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.
6) RELEASE DATE:
Tue Feb 14 16:40:29 PST 2012 By Kecia Duffy - [email protected]
7) AUTHORS:
For additional information, please contact:
Stephan Trong - [email protected]
James Han - [email protected]
This file was automatically generated by the single cell pipeline software (version 1.1.8).
|
| 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 | Host Associated | |
| 3 | Proteobacteria |
