Seq. Project name:
Actinobaculum schaalii DSM 15541
( Project ID: 1012037 )
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: | Actinotignum / Actinotignum schaalii / DSM 15541 / |
| GOLD ID: | Gp0013925 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1012037
Actinobaculum schaalii DSM 15541
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
HPPC 8122984 2x150 Illumina Std PE (cassava 1.8) 6501.1.45839.ATCTAT.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: 8122984 (100%)
Artifact reads removed: 702014 (8.6%)
Total reads removed: 702014 (8.6%)
Total reads remaining: 7420970 (91.4%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 8122984 (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: 59.32 +/- 3.57%
Largest Contig: 405.0 KB
Main genome scaffold total: 32
Main genome contig total: 35
Main genome scaffold sequence total: 2.1 MB
Main genome contig sequence total: 2.1 MB (-> 0.0% gap)
Main genome scaffold N/L50: 4/149.2 KB
Main genome contig N/L50: 4/149.2 KB
Number of scaffolds > 50 KB: 11
% main genome in scaffolds > 50 KB: 88.5%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 32 35 2,135,758 2,135,356 99.98%
1 kb 25 28 2,131,100 2,130,698 99.98%
2.5 kb 23 26 2,128,445 2,128,043 99.98%
5 kb 19 22 2,115,953 2,115,551 99.98%
10 kb 18 21 2,110,942 2,110,540 99.98%
25 kb 17 20 2,099,983 2,099,581 99.98%
50 kb 11 14 1,891,140 1,890,748 99.98%
100 kb 8 11 1,641,888 1,641,522 99.98%
250 kb 2 2 748,389 748,309 99.99%
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: 59.62 +/- 3.77%
Largest Contig: 403.1 KB
Main genome scaffold total: 27
Main genome contig total: 29
Main genome scaffold sequence total: 2.1 MB
Main genome contig sequence total: 2.1 MB (-> 0.1% gap)
Main genome scaffold N/L50: 4/149.3 KB
Main genome contig N/L50: 5/138.2 KB
Number of scaffolds > 50 KB: 11
% main genome in scaffolds > 50 KB: 88.8%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 27 29 2,130,987 2,129,678 99.94%
1 kb 27 29 2,130,987 2,129,678 99.94%
2.5 kb 20 22 2,120,736 2,119,427 99.94%
5 kb 18 20 2,115,040 2,113,731 99.94%
10 kb 18 20 2,115,040 2,113,731 99.94%
25 kb 17 19 2,103,775 2,102,466 99.94%
50 kb 11 13 1,893,118 1,891,809 99.93%
100 kb 9 10 1,743,478 1,743,378 99.99%
250 kb 2 3 747,955 747,855 99.99%
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 14:55:55 PDT 2013 By Kecia Duffy- [email protected]
9) AUTHORS:
For additional information, please contact:
Kecia Duffy - [email protected]
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 | Actinobacteria | |
| 2 | Host Associated |
