Seq. Project name:
Streptomyces sp. CNT360
( Project ID: 1016046 )
Product:
Microbial Minimal Draft, Isolate
Proposal Name:
Multiplexed sequencing for secondary metabolite discovery
(Proposal ID: 644)
Project PI:
User Program:
CSP
Program Year:
2010
Scientific Program:
Microbial
Release Date:
2013-05-31
Organism | |
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Genus/species/strain/isolate: | Streptomyces / Streptomyces sp. / CNT360 / |
GOLD ID: | Gp0033431 |
Contacts | |
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JGI: | |
Request DNA: | Paul robert Jensen <[email protected]> |
General Information | |
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QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1016046
Streptomyces sp.
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 30433616 2x150 Illumina Std PE (cassava 1.8) 6585.1.48173.CCGTCC.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: 30433616 (100%)
Artifact reads removed: 144874 (0.5%)
Total reads removed: 144874 (0.5%)
Total reads remaining: 30288742 (99.5%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 30433616 (100%)
Num contam reads identified: 778 (0.0%)
- Pseudomonas 772 0.00%
- Ralstonia 4 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: 69.91 +/- 4.61%
Largest Contig: 735.0 KB
Main genome scaffold total: 58
Main genome contig total: 86
Main genome scaffold sequence total: 7.7 MB
Main genome contig sequence total: 7.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 8/328.9 KB
Main genome contig N/L50: 11/205.4 KB
Number of scaffolds > 50 KB: 31
% main genome in scaffolds > 50 KB: 97.3%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 58 86 7,725,418 7,721,375 99.95%
1 kb 49 77 7,719,209 7,715,166 99.95%
2.5 kb 43 71 7,711,184 7,707,141 99.95%
5 kb 38 66 7,692,473 7,688,430 99.95%
10 kb 36 64 7,676,174 7,672,131 99.95%
25 kb 34 62 7,644,636 7,640,593 99.95%
50 kb 31 59 7,515,697 7,511,654 99.95%
100 kb 25 52 7,024,385 7,020,464 99.94%
250 kb 11 30 4,734,472 4,731,664 99.94%
500 kb 3 9 2,060,892 2,059,905 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: 71.69 +/- 2.27%
Largest Contig: 1053.4 KB
Main genome scaffold total: 41
Main genome contig total: 51
Main genome scaffold sequence total: 7.7 MB
Main genome contig sequence total: 7.7 MB (-> 0.1% gap)
Main genome scaffold N/L50: 7/365.2 KB
Main genome contig N/L50: 7/301.0 KB
Number of scaffolds > 50 KB: 27
% main genome in scaffolds > 50 KB: 97.6%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 41 51 7,720,660 7,710,989 99.87%
1 kb 41 51 7,720,660 7,710,989 99.87%
2.5 kb 37 47 7,714,992 7,705,321 99.87%
5 kb 34 44 7,704,794 7,695,123 99.87%
10 kb 32 42 7,691,930 7,682,259 99.87%
25 kb 30 40 7,651,851 7,642,180 99.87%
50 kb 27 37 7,531,526 7,521,855 99.87%
100 kb 22 31 7,102,706 7,093,490 99.87%
250 kb 10 17 5,115,342 5,106,863 99.83%
500 kb 4 4 3,032,520 3,032,510 100.00%
1 mb 1 1 1,053,426 1,053,416 100.00%
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:
Tue Apr 23 15:08:12 PDT 2013 By Hui Sun- [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 | |
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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 |
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## | Name | Type |
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1 | Actinobacteria |