Seq. Project name:
Silanimonas lenta DSM 16282
( Project ID: 1008580 )
Product:
Microbial Minimal Draft, Isolate
Proposal Name:
Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
(Proposal ID: 733)
Project PI:
User Program:
CSP
Program Year:
2012
Scientific Program:
Microbial
Release Date:
2013-05-31
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Silanimonas / Silanimonas lenta / DSM 16282 / |
| GOLD ID: | Gp0013280 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1008580
Silanimonas lenta DSM 16282
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
HPNW 17980428 2x150 Illumina Std PE (cassava 1.8) 6501.2.45840.TGCCAT.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: 17980428 (100%)
Artifact reads removed: 4 (0.0%)
Total reads removed: 4 (0.0%)
Total reads remaining: 17980424 (100.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 17980428 (100%)
Num contam reads identified: 2604 (0.0%)
- Ralstonia 1808 0.01%
- Pseudomonas 792 0.00%
- Cupriavidus 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: 69.21 +/- 3.69%
Largest Contig: 500.8 KB
Main genome scaffold total: 32
Main genome contig total: 44
Main genome scaffold sequence total: 2.7 MB
Main genome contig sequence total: 2.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 4/289.4 KB
Main genome contig N/L50: 5/182.7 KB
Number of scaffolds > 50 KB: 11
% main genome in scaffolds > 50 KB: 94.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 32 44 2,664,494 2,662,996 99.94%
1 kb 32 44 2,664,494 2,662,996 99.94%
2.5 kb 22 34 2,650,566 2,649,068 99.94%
5 kb 19 31 2,640,915 2,639,417 99.94%
10 kb 16 28 2,619,072 2,617,574 99.94%
25 kb 13 24 2,570,901 2,569,469 99.94%
50 kb 11 21 2,504,542 2,503,229 99.95%
100 kb 9 16 2,399,137 2,398,036 99.95%
250 kb 5 10 1,780,892 1,780,017 99.95%
500 kb 1 1 500,812 500,656 99.97%
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: 69.32 +/- 3.80%
Largest Contig: 540.5 KB
Main genome scaffold total: 21
Main genome contig total: 24
Main genome scaffold sequence total: 2.6 MB
Main genome contig sequence total: 2.6 MB (-> 0.1% gap)
Main genome scaffold N/L50: 3/321.6 KB
Main genome contig N/L50: 4/279.4 KB
Number of scaffolds > 50 KB: 9
% main genome in scaffolds > 50 KB: 91.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 21 24 2,647,044 2,644,563 99.91%
1 kb 21 24 2,647,044 2,644,563 99.91%
2.5 kb 19 22 2,644,078 2,641,597 99.91%
5 kb 19 22 2,644,078 2,641,597 99.91%
10 kb 16 19 2,620,150 2,617,669 99.91%
25 kb 14 17 2,583,775 2,581,294 99.90%
50 kb 9 12 2,408,423 2,405,942 99.90%
100 kb 8 11 2,353,549 2,351,068 99.89%
250 kb 5 8 1,932,106 1,929,625 99.87%
500 kb 2 4 1,041,386 1,039,470 99.82%
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:
Fri May 17 12:41:44 PDT 2013 By Kecia Duffy- [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).
|
| 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 | Environmental | |
| 2 | Gammaproteobacteria | |
| 3 | Proteobacteria |
