Seq. Project name:
Moraxella caprae DSM 19149
( Project ID: 1006784 )
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: | Moraxella / Moraxella caprae / DSM 19149 / |
| GOLD ID: | Gp0013058 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1006784
Moraxella caprae DSM 19149
1) RAW DATA:
LibraryName NumReads ReadType FileName
CXUS 11267044 2x150 6176.4.39296.AACTTG.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: 11267044 (100%)
Artifact reads removed: 512230 (4.5%)
Total reads removed: 512230 (4.5%)
Total reads remaining: 10754814 (95.5%)
3) STD READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 11267044 (100%)
Num contam reads identified: 2506 (0.0%)
- Pseudomonas 1296 0.01%
- Ralstonia 1203 0.01%
- Klebsiella 5 0.00%
- Delftia 2 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: 41.89 +/- 4.43%
Largest Contig: 157.8 KB
Main genome scaffold total: 127
Main genome contig total: 132
Main genome scaffold sequence total: 2.6 MB
Main genome contig sequence total: 2.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 13/73.7 KB
Main genome contig N/L50: 15/52.0 KB
Number of scaffolds > 50 KB: 16
% main genome in scaffolds > 50 KB: 57.3%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 127 132 2,583,751 2,583,064 99.97%
1 kb 112 117 2,572,397 2,571,710 99.97%
2.5 kb 91 96 2,537,822 2,537,135 99.97%
5 kb 64 69 2,440,751 2,440,064 99.97%
10 kb 51 56 2,350,677 2,349,990 99.97%
25 kb 29 32 1,977,117 1,976,572 99.97%
50 kb 16 19 1,480,433 1,479,908 99.96%
100 kb 6 8 696,261 695,874 99.94%
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: 42.48 +/- 3.80%
Largest Contig: 158.2 KB
Main genome scaffold total: 108
Main genome contig total: 108
Main genome scaffold sequence total: 2.6 MB
Main genome contig sequence total: 2.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 14/64.0 KB
Main genome contig N/L50: 14/64.0 KB
Number of scaffolds > 50 KB: 15
% main genome in scaffolds > 50 KB: 53.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 108 108 2,600,132 2,600,132 100.00%
1 kb 107 107 2,599,756 2,599,756 100.00%
2.5 kb 89 89 2,568,188 2,568,188 100.00%
5 kb 72 72 2,507,667 2,507,667 100.00%
10 kb 56 56 2,390,377 2,390,377 100.00%
25 kb 30 30 1,954,442 1,954,442 100.00%
50 kb 15 15 1,379,274 1,379,274 100.00%
100 kb 6 6 679,776 679,776 100.00%
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:
Mon Apr 1 11:55:11 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 | Gammaproteobacteria | |
| 2 | Host Associated | |
| 3 | Proteobacteria |
