Seq. Project name:
Glaciibacter superstes DSM 21135
( Project ID: 1013846 )
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: | Glaciibacter / Glaciibacter superstes / DSM 21135 / |
| GOLD ID: | Gp0013647 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1013846
Glaciibacter superstes DSM 21135
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 10837582 2x150 Illumina Std PE (cassava 1.8) 6740.1.52790.TGCTGG.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: 10837582 (100%)
Artifact reads removed: 277852 (2.6%)
Total reads removed: 277852 (2.6%)
Total reads remaining: 10559730 (97.4%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 10837582 (100%)
Num contam reads identified: 2 (0.0%)
- Ralstonia 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: 63.02 +/- 3.03%
Largest Contig: 434.3 KB
Main genome scaffold total: 51
Main genome contig total: 75
Main genome scaffold sequence total: 4.8 MB
Main genome contig sequence total: 4.8 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/253.1 KB
Main genome contig N/L50: 11/150.4 KB
Number of scaffolds > 50 KB: 20
% 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 51 75 4,774,742 4,772,410 99.95%
1 kb 43 67 4,769,485 4,767,153 99.95%
2.5 kb 36 60 4,758,621 4,756,289 99.95%
5 kb 32 56 4,741,357 4,739,025 99.95%
10 kb 31 55 4,735,679 4,733,347 99.95%
25 kb 24 48 4,616,544 4,614,212 99.95%
50 kb 20 44 4,490,251 4,487,919 99.95%
100 kb 16 40 4,224,907 4,222,575 99.94%
250 kb 7 20 2,481,954 2,480,615 99.95%
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: 63.80 +/- 2.06%
Largest Contig: 435.1 KB
Main genome scaffold total: 38
Main genome contig total: 38
Main genome scaffold sequence total: 4.8 MB
Main genome contig sequence total: 4.8 MB (-> 0.0% gap)
Main genome scaffold N/L50: 7/254.7 KB
Main genome contig N/L50: 7/254.7 KB
Number of scaffolds > 50 KB: 20
% 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 38 38 4,802,534 4,802,524 100.00%
1 kb 38 38 4,802,534 4,802,524 100.00%
2.5 kb 35 35 4,797,759 4,797,749 100.00%
5 kb 33 33 4,789,845 4,789,835 100.00%
10 kb 31 31 4,774,445 4,774,435 100.00%
25 kb 25 25 4,675,518 4,675,508 100.00%
50 kb 20 20 4,521,909 4,521,899 100.00%
100 kb 16 16 4,253,439 4,253,429 100.00%
250 kb 7 7 2,494,273 2,494,273 100.00%
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 Apr 22 09:39:12 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 |
