Seq. Project name:
Arenimonas composti DSM 18010
( Project ID: 1013984 )
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: | Arenimonas / Arenimonas composti / DSM 18010 / |
| GOLD ID: | Gp0013401 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1013984
Arenimonas composti DSM 18010
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 4145892 2x150 Illumina Std PE (cassava 1.8) 6740.1.52790.GGCCTG.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: 4145892 (100%)
Artifact reads removed: 136806 (3.3%)
Total reads removed: 136806 (3.3%)
Total reads remaining: 4009086 (96.7%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 4145892 (100%)
Num contam reads identified: 1126 (0.0%)
- Ralstonia 854 0.02%
- Pseudomonas 270 0.01%
- Cupriavidus 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: 65.18 +/- 5.87%
Largest Contig: 946.9 KB
Main genome scaffold total: 44
Main genome contig total: 51
Main genome scaffold sequence total: 3.2 MB
Main genome contig sequence total: 3.2 MB (-> 0.0% gap)
Main genome scaffold N/L50: 3/542.8 KB
Main genome contig N/L50: 3/207.7 KB
Number of scaffolds > 50 KB: 11
% main genome in scaffolds > 50 KB: 95.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 44 51 3,167,639 3,166,859 99.98%
1 kb 32 39 3,159,584 3,158,804 99.98%
2.5 kb 22 29 3,145,333 3,144,553 99.98%
5 kb 18 25 3,131,339 3,130,559 99.98%
10 kb 15 22 3,110,184 3,109,404 99.97%
25 kb 13 20 3,081,857 3,081,077 99.97%
50 kb 11 18 3,009,149 3,008,369 99.97%
100 kb 6 13 2,628,996 2,628,296 99.97%
250 kb 3 8 2,091,182 2,090,701 99.98%
500 kb 3 8 2,091,182 2,090,701 99.98%
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: 65.79 +/- 6.27%
Largest Contig: 947.5 KB
Main genome scaffold total: 29
Main genome contig total: 29
Main genome scaffold sequence total: 3.2 MB
Main genome contig sequence total: 3.2 MB (-> 0.0% gap)
Main genome scaffold N/L50: 3/544.3 KB
Main genome contig N/L50: 3/544.3 KB
Number of scaffolds > 50 KB: 12
% main genome in scaffolds > 50 KB: 96.9%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 29 29 3,159,341 3,159,316 100.00%
1 kb 29 29 3,159,341 3,159,316 100.00%
2.5 kb 20 20 3,143,802 3,143,777 100.00%
5 kb 16 16 3,130,347 3,130,322 100.00%
10 kb 16 16 3,130,347 3,130,322 100.00%
25 kb 13 13 3,090,450 3,090,425 100.00%
50 kb 12 12 3,061,419 3,061,394 100.00%
100 kb 6 6 2,622,739 2,622,714 100.00%
250 kb 3 3 2,040,787 2,040,777 100.00%
500 kb 3 3 2,040,787 2,040,777 100.00%
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:
Fri Apr 19 13:22:58 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 | Engineered | |
| 2 | Gammaproteobacteria | |
| 3 | Proteobacteria |
