Seq. Project name:
Bacteroides graminisolvens DSM 19988
( Project ID: 1000025 )
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: | Bacteroides / Bacteroides graminisolvens / DSM 19988 / |
| GOLD ID: | Gp0013529 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1000025
Bacteroides graminisolvens DSM 19988
1) RAW DATA:
LibraryName NumReads ReadType FileName
CXGU 6936462 2x150 6175.1.39285.TTAGGC.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: 6936462 (100%)
Artifact reads removed: 183178 (2.6%)
Total reads removed: 183178 (2.6%)
Total reads remaining: 6753284 (97.4%)
3) STD READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 6936462 (100%)
Num contam reads identified: 5 (0.0%)
- Pseudomonas 4 0.00%
- Ralstonia 1 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: 40.92 +/- 3.52%
Largest Contig: 1167.9 KB
Main genome scaffold total: 39
Main genome contig total: 49
Main genome scaffold sequence total: 3.7 MB
Main genome contig sequence total: 3.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 3/203.2 KB
Main genome contig N/L50: 3/183.1 KB
Number of scaffolds > 50 KB: 15
% main genome in scaffolds > 50 KB: 90.2%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 39 49 3,690,267 3,688,974 99.96%
1 kb 35 45 3,687,327 3,686,034 99.96%
2.5 kb 29 39 3,677,487 3,676,194 99.96%
5 kb 25 35 3,664,511 3,663,218 99.96%
10 kb 25 35 3,664,511 3,663,218 99.96%
25 kb 22 32 3,626,123 3,624,840 99.96%
50 kb 15 24 3,329,290 3,328,149 99.97%
100 kb 9 17 2,906,801 2,905,765 99.96%
250 kb 2 4 1,836,206 1,835,848 99.98%
500 kb 2 4 1,836,206 1,835,848 99.98%
1 mb 1 1 1,167,863 1,167,813 100.00%
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: 40.27 +/- 2.56%
Largest Contig: 1114.3 KB
Main genome scaffold total: 34
Main genome contig total: 34
Main genome scaffold sequence total: 3.6 MB
Main genome contig sequence total: 3.6 MB (-> 0.0% gap)
Main genome scaffold N/L50: 4/196.5 KB
Main genome contig N/L50: 4/196.5 KB
Number of scaffolds > 50 KB: 16
% main genome in scaffolds > 50 KB: 90.3%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 34 34 3,631,399 3,631,399 100.00%
1 kb 33 33 3,631,099 3,631,099 100.00%
2.5 kb 29 29 3,624,350 3,624,350 100.00%
5 kb 27 27 3,618,772 3,618,772 100.00%
10 kb 26 26 3,613,342 3,613,342 100.00%
25 kb 23 23 3,574,417 3,574,417 100.00%
50 kb 16 16 3,277,550 3,277,550 100.00%
100 kb 10 10 2,854,379 2,854,379 100.00%
250 kb 2 2 1,585,326 1,585,326 100.00%
500 kb 1 1 1,114,263 1,114,263 100.00%
1 mb 1 1 1,114,263 1,114,263 100.00%
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:
Tue Apr 23 10:04:23 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 | Bacteroidetes | |
| 2 | Host Associated |
