Seq. Project name:
Serinicoccus marinus DSM 15273
( Project ID: 1013954 )
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: | Serinicoccus / Serinicoccus marinus / DSM 15273 / |
| GOLD ID: | Gp0013278 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1013954
Serinicoccus marinus DSM 15273
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 8321620 2x150 Illumina Std PE (cassava 1.8) 6740.1.52790.TTCTCC.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: 8321620 (100%)
Artifact reads removed: 84276 (1.0%)
Total reads removed: 84276 (1.0%)
Total reads remaining: 8237344 (99.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 8321620 (100%)
Num contam reads identified: 8 (0.0%)
- Cupriavidus 4 0.00%
- Delftia 2 0.00%
- Vibrio 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: 68.42 +/- 4.58%
Largest Contig: 490.1 KB
Main genome scaffold total: 39
Main genome contig total: 42
Main genome scaffold sequence total: 3.4 MB
Main genome contig sequence total: 3.4 MB (-> 0.0% gap)
Main genome scaffold N/L50: 4/377.7 KB
Main genome contig N/L50: 4/377.7 KB
Number of scaffolds > 50 KB: 12
% 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 39 42 3,398,321 3,397,961 99.99%
1 kb 35 38 3,395,344 3,394,984 99.99%
2.5 kb 22 25 3,375,948 3,375,598 99.99%
5 kb 20 23 3,368,685 3,368,335 99.99%
10 kb 17 20 3,347,759 3,347,409 99.99%
25 kb 15 18 3,315,260 3,314,910 99.99%
50 kb 12 15 3,193,560 3,193,210 99.99%
100 kb 10 13 3,020,816 3,020,466 99.99%
250 kb 5 7 2,078,730 2,078,484 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: 69.33 +/- 4.21%
Largest Contig: 490.8 KB
Main genome scaffold total: 29
Main genome contig total: 29
Main genome scaffold sequence total: 3.4 MB
Main genome contig sequence total: 3.4 MB (-> 0.0% gap)
Main genome scaffold N/L50: 4/378.2 KB
Main genome contig N/L50: 4/378.2 KB
Number of scaffolds > 50 KB: 12
% main genome in scaffolds > 50 KB: 94.2%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 29 29 3,396,505 3,396,505 100.00%
1 kb 29 29 3,396,505 3,396,505 100.00%
2.5 kb 21 21 3,384,866 3,384,866 100.00%
5 kb 20 20 3,380,026 3,380,026 100.00%
10 kb 18 18 3,367,748 3,367,748 100.00%
25 kb 15 15 3,322,843 3,322,843 100.00%
50 kb 12 12 3,199,464 3,199,464 100.00%
100 kb 10 10 3,024,793 3,024,793 100.00%
250 kb 5 5 2,081,580 2,081,580 100.00%
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 May 13 10:17:43 PDT 2013 By Andrew Tritt- [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 | Actinobacteria | |
| 2 | Environmental |
