Seq. Project name:
Patulibacter americanus DSM 16676
( Project ID: 1002989 )
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: | Patulibacter / Patulibacter americanus / DSM 16676 / |
| GOLD ID: | Gp0013117 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1002989
Patulibacter americanus DSM 16676
1) RAW DATA:
LibraryName NumReads ReadType FileName
CXHH 10861836 2x150 6175.1.39285.CGTACG.fastq
2) STD 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: 10861836 (100%)
Artifact reads removed: 83096 (0.8%)
Total reads removed: 83096 (0.8%)
Total reads remaining: 10778740 (99.2%)
3) STD READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 10861836 (100%)
Num contam reads identified: 1 (0.0%)
- Ralstonia 1 0.00%
4) ASSEMBLY STATS:
a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer. The input reads have been filtered for artifacts.
Avg GC Content: 57.16 +/- 21.86%
Largest Contig: 50.9 KB
Main genome scaffold total: 1080
Main genome contig total: 1082
Main genome scaffold sequence total: 4.7 MB
Main genome contig sequence total: 4.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 109/13.1 KB
Main genome contig N/L50: 109/13.1 KB
Number of scaffolds > 50 KB: 1
% main genome in scaffolds > 50 KB: 1.1%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 1,080 1,082 4,675,957 4,675,735 100.00%
1 kb 571 571 4,344,261 4,344,261 100.00%
2.5 kb 394 394 4,075,473 4,075,473 100.00%
5 kb 268 268 3,612,218 3,612,218 100.00%
10 kb 143 143 2,734,366 2,734,366 100.00%
25 kb 28 28 880,768 880,768 100.00%
50 kb 1 1 50,858 50,858 100.00%
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: 72.80 +/- 4.70%
Largest Contig: 888.9 KB
Main genome scaffold total: 32
Main genome contig total: 32
Main genome scaffold sequence total: 4.5 MB
Main genome contig sequence total: 4.5 MB (-> 0.0% gap)
Main genome scaffold N/L50: 5/279.5 KB
Main genome contig N/L50: 5/279.5 KB
Number of scaffolds > 50 KB: 18
% main genome in scaffolds > 50 KB: 94.6%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 32 32 4,470,560 4,470,560 100.00%
1 kb 32 32 4,470,560 4,470,560 100.00%
2.5 kb 27 27 4,462,717 4,462,717 100.00%
5 kb 25 25 4,453,705 4,453,705 100.00%
10 kb 25 25 4,453,705 4,453,705 100.00%
25 kb 23 23 4,424,671 4,424,671 100.00%
50 kb 18 18 4,228,117 4,228,117 100.00%
100 kb 13 13 3,833,774 3,833,774 100.00%
250 kb 7 7 2,872,062 2,872,062 100.00%
500 kb 1 1 888,876 888,876 100.00%
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: r41043
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,1,200,35,,,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) RELEASE DATE:
Tue Apr 23 14:46:23 PDT 2013 By Alexander Spunde- [email protected]
8) 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 2.0.7).
|
| 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 |
