Seq. Project name:
Helcococcus sueciensis DSM 17243
( Project ID: 1012067 )
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: | Helcococcus / Helcococcus sueciensis / DSM 17243 / |
| GOLD ID: | Gp0013706 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1012067
Helcococcus sueciensis DSM 17243
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
HPSA 25210548 2x150 Illumina Std PE (cassava 1.8) 6501.1.45839.AGAAGA.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: 25210548 (100%)
Artifact reads removed: 32 (0.0%)
Total reads removed: 32 (0.0%)
Total reads remaining: 25210516 (100.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 25210548 (100%)
Num contam reads identified: 0 (0.0%)
4) ASSEMBLY STATS:
a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer.
Avg GC Content: 30.10 +/- 4.33%
Largest Contig: 125.5 KB
Main genome scaffold total: 54
Main genome contig total: 56
Main genome scaffold sequence total: 1.6 MB
Main genome contig sequence total: 1.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 9/74.5 KB
Main genome contig N/L50: 9/74.5 KB
Number of scaffolds > 50 KB: 13
% main genome in scaffolds > 50 KB: 65.6%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 54 56 1,568,294 1,568,016 99.98%
1 kb 48 50 1,564,370 1,564,092 99.98%
2.5 kb 38 40 1,549,107 1,548,839 99.98%
5 kb 38 40 1,549,107 1,548,839 99.98%
10 kb 31 33 1,498,099 1,497,831 99.98%
25 kb 21 21 1,333,779 1,333,759 100.00%
50 kb 13 13 1,028,625 1,028,615 100.00%
100 kb 2 2 227,142 227,142 100.00%
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: 29.34 +/- 3.58%
Largest Contig: 127.6 KB
Main genome scaffold total: 43
Main genome contig total: 45
Main genome scaffold sequence total: 1.6 MB
Main genome contig sequence total: 1.6 MB (-> 0.1% gap)
Main genome scaffold N/L50: 9/75.0 KB
Main genome contig N/L50: 9/75.0 KB
Number of scaffolds > 50 KB: 13
% main genome in scaffolds > 50 KB: 65.8%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 43 45 1,573,767 1,572,792 99.94%
1 kb 43 45 1,573,767 1,572,792 99.94%
2.5 kb 38 40 1,565,932 1,564,957 99.94%
5 kb 38 40 1,565,932 1,564,957 99.94%
10 kb 31 33 1,511,710 1,510,735 99.94%
25 kb 21 23 1,343,488 1,342,513 99.93%
50 kb 13 14 1,035,108 1,034,223 99.91%
100 kb 2 2 229,593 229,593 100.00%
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:
Wed May 8 10:26:34 PDT 2013 By Kecia Duffy- [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).
|
| 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 | Firmicutes | |
| 2 | Host Associated |
