Seq. Project name:
Saccharospirillum impatiens DSM 12546
( Project ID: 1010758 )
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: | Saccharospirillum / Saccharospirillum impatiens / DSM 12546 / |
| GOLD ID: | Gp0013243 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1010758
Saccharospirillum impatiens DSM 12546
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 8943836 2x150 Illumina Std PE (cassava 1.8) 6501.3.45841.AGTCAA.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: 8943836 (100%)
Artifact reads removed: 4 (0.0%)
Total reads removed: 4 (0.0%)
Total reads remaining: 8943832 (100.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 8943836 (100%)
Num contam reads identified: 906 (0.0%)
- Ralstonia 890 0.01%
- Pseudomonas 10 0.00%
- Delftia 6 0.00%
4) ASSEMBLY STATS:
a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer.
Avg GC Content: 51.51 +/- 5.10%
Largest Contig: 278.5 KB
Main genome scaffold total: 203
Main genome contig total: 211
Main genome scaffold sequence total: 4.7 MB
Main genome contig sequence total: 4.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 13/110.1 KB
Main genome contig N/L50: 16/86.1 KB
Number of scaffolds > 50 KB: 26
% main genome in scaffolds > 50 KB: 71.9%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 203 211 4,741,036 4,740,016 99.98%
1 kb 163 171 4,713,363 4,712,343 99.98%
2.5 kb 116 124 4,632,842 4,631,857 99.98%
5 kb 91 99 4,542,441 4,541,456 99.98%
10 kb 63 71 4,340,446 4,339,501 99.98%
25 kb 42 49 4,000,073 3,999,179 99.98%
50 kb 26 32 3,409,106 3,408,298 99.98%
100 kb 15 20 2,615,964 2,615,432 99.98%
250 kb 2 3 537,634 537,574 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: 52.25 +/- 4.68%
Largest Contig: 279.1 KB
Main genome scaffold total: 148
Main genome contig total: 154
Main genome scaffold sequence total: 4.7 MB
Main genome contig sequence total: 4.7 MB (-> 0.1% gap)
Main genome scaffold N/L50: 13/110.4 KB
Main genome contig N/L50: 13/110.4 KB
Number of scaffolds > 50 KB: 26
% main genome in scaffolds > 50 KB: 72.3%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 148 154 4,743,148 4,736,515 99.86%
1 kb 148 154 4,743,148 4,736,515 99.86%
2.5 kb 113 119 4,680,077 4,673,444 99.86%
5 kb 95 101 4,615,980 4,609,347 99.86%
10 kb 67 72 4,420,144 4,415,431 99.89%
25 kb 42 46 4,026,066 4,021,698 99.89%
50 kb 26 30 3,428,144 3,423,776 99.87%
100 kb 15 17 2,623,655 2,619,557 99.84%
250 kb 2 2 538,996 538,986 100.00%
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 6 12:39:23 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 2.1.2.1).
|
| 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 | Environmental | |
| 2 | Gammaproteobacteria | |
| 3 | Proteobacteria |
