Seq. Project name:
Nakamurella lactea DSM 19367
( Project ID: 1013771 )
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: | Nakamurella / Nakamurella lactea / DSM 19367 / |
| GOLD ID: | Gp0013256 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1013771
Saxeibacter lacteus DSM 19367
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 13910936 2x150 Illumina Std PE (cassava 1.8) 6740.1.52790.GATGCT.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: 13910936 (100%)
Artifact reads removed: 148698 (1.1%)
Total reads removed: 148698 (1.1%)
Total reads remaining: 13762238 (98.9%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 13910936 (100%)
Num contam reads identified: 4 (0.0%)
- Escherichia 2 0.00%
- 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: 68.20 +/- 1.81%
Largest Contig: 686.8 KB
Main genome scaffold total: 34
Main genome contig total: 40
Main genome scaffold sequence total: 5.8 MB
Main genome contig sequence total: 5.8 MB (-> 0.0% gap)
Main genome scaffold N/L50: 6/363.9 KB
Main genome contig N/L50: 6/363.9 KB
Number of scaffolds > 50 KB: 22
% main genome in scaffolds > 50 KB: 98.1%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 34 40 5,819,055 5,818,397 99.99%
1 kb 32 38 5,817,348 5,816,690 99.99%
2.5 kb 26 32 5,809,244 5,808,586 99.99%
5 kb 26 32 5,809,244 5,808,586 99.99%
10 kb 26 32 5,809,244 5,808,586 99.99%
25 kb 24 29 5,781,470 5,780,893 99.99%
50 kb 22 27 5,705,651 5,705,074 99.99%
100 kb 20 23 5,571,690 5,571,323 99.99%
250 kb 10 12 4,079,413 4,079,177 99.99%
500 kb 2 2 1,212,543 1,212,543 100.00%
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: 68.32 +/- 1.54%
Largest Contig: 686.9 KB
Main genome scaffold total: 27
Main genome contig total: 31
Main genome scaffold sequence total: 5.8 MB
Main genome contig sequence total: 5.8 MB (-> 0.0% gap)
Main genome scaffold N/L50: 6/454.7 KB
Main genome contig N/L50: 6/454.7 KB
Number of scaffolds > 50 KB: 20
% main genome in scaffolds > 50 KB: 98.1%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 27 31 5,820,860 5,819,110 99.97%
1 kb 27 31 5,820,860 5,819,110 99.97%
2.5 kb 24 28 5,816,998 5,815,248 99.97%
5 kb 24 28 5,816,998 5,815,248 99.97%
10 kb 24 28 5,816,998 5,815,248 99.97%
25 kb 22 26 5,788,696 5,786,946 99.97%
50 kb 20 24 5,711,384 5,709,634 99.97%
100 kb 18 22 5,576,388 5,574,638 99.97%
250 kb 9 12 4,083,660 4,083,215 99.99%
500 kb 3 5 1,809,059 1,808,709 99.98%
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 12:59:21 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 |
