Seq. Project name:
Globicatella sulfidifaciens DSM 15739
( Project ID: 1012061 )
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: | Globicatella / Globicatella sulfidifaciens / DSM 15739 / |
| GOLD ID: | Gp0013648 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1012061
Globicatella sulfidifaciens DSM 15739
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
HPPU 42616608 2x150 Illumina Std PE (cassava 1.8) 6500.7.45807.TCGGCA.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: 42616608 (100%)
Artifact reads removed: 24 (0.0%)
Total reads removed: 24 (0.0%)
Total reads remaining: 42616584 (100.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 42616608 (100%)
Num contam reads identified: 16 (0.0%)
- Escherichia 6 0.00%
- Pseudomonas 4 0.00%
- Cupriavidus 2 0.00%
- Delftia 2 0.00%
- Shigella 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: 37.09 +/- 4.52%
Largest Contig: 244.9 KB
Main genome scaffold total: 50
Main genome contig total: 54
Main genome scaffold sequence total: 2.2 MB
Main genome contig sequence total: 2.2 MB (-> 0.0% gap)
Main genome scaffold N/L50: 8/99.1 KB
Main genome contig N/L50: 8/99.0 KB
Number of scaffolds > 50 KB: 18
% main genome in scaffolds > 50 KB: 85.2%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 50 54 2,212,649 2,212,179 99.98%
1 kb 43 47 2,208,642 2,208,172 99.98%
2.5 kb 37 41 2,197,986 2,197,516 99.98%
5 kb 35 39 2,190,814 2,190,344 99.98%
10 kb 31 35 2,165,614 2,165,144 99.98%
25 kb 22 26 2,016,828 2,016,358 99.98%
50 kb 18 22 1,884,589 1,884,129 99.98%
100 kb 7 8 1,101,506 1,101,421 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: 35.46 +/- 1.23%
Largest Contig: 245.0 KB
Main genome scaffold total: 38
Main genome contig total: 45
Main genome scaffold sequence total: 2.2 MB
Main genome contig sequence total: 2.2 MB (-> 0.1% gap)
Main genome scaffold N/L50: 7/106.5 KB
Main genome contig N/L50: 8/99.1 KB
Number of scaffolds > 50 KB: 17
% main genome in scaffolds > 50 KB: 85.3%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 38 45 2,215,522 2,212,224 99.85%
1 kb 38 45 2,215,522 2,212,224 99.85%
2.5 kb 37 44 2,213,571 2,210,273 99.85%
5 kb 34 41 2,203,830 2,200,532 99.85%
10 kb 30 37 2,177,481 2,174,183 99.85%
25 kb 22 29 2,048,534 2,045,236 99.84%
50 kb 17 24 1,890,103 1,886,805 99.83%
100 kb 7 10 1,157,584 1,155,677 99.84%
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:
Tue Apr 30 14:04:20 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).
|
| 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 | Firmicutes | |
| 2 | Host Associated |
