Seq. Project name:
Selenomonas ruminantium ATCC 12561
( Project ID: 1012743 )
Product:
Microbial Minimal Draft, Isolate
Proposal Name:
The Hungate 1000. A catalogue of reference genomes from the rumen microbiome.
(Proposal ID: 612)
Project PI:
User Program:
CSP
Program Year:
2012
Scientific Program:
Microbial
Release Date:
2013-05-31
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Selenomonas / Selenomonas ruminantium / ATCC 12561 / |
| GOLD ID: | Gp0025721 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | William Kelly <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1012743
Selenomonas ruminantium
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
HCBY 9917010 2x150 Illumina Std PE (cassava 1.8) 6513.2.46682.CAAAAG.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: 9917010 (100%)
Artifact reads removed: 2 (0.0%)
Total reads removed: 2 (0.0%)
Total reads remaining: 9917008 (100.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 9917010 (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: 47.30 +/- 3.67%
Largest Contig: 178.5 KB
Main genome scaffold total: 94
Main genome contig total: 104
Main genome scaffold sequence total: 3.4 MB
Main genome contig sequence total: 3.4 MB (-> 0.0% gap)
Main genome scaffold N/L50: 15/82.8 KB
Main genome contig N/L50: 16/75.9 KB
Number of scaffolds > 50 KB: 28
% main genome in scaffolds > 50 KB: 76.5%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 94 104 3,393,649 3,392,274 99.96%
1 kb 77 87 3,381,402 3,380,037 99.96%
2.5 kb 67 76 3,364,328 3,363,077 99.96%
5 kb 63 72 3,348,411 3,347,160 99.96%
10 kb 57 65 3,301,921 3,300,838 99.97%
25 kb 39 47 2,993,476 2,992,433 99.97%
50 kb 28 33 2,595,630 2,594,960 99.97%
100 kb 11 16 1,430,960 1,430,310 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: 47.73 +/- 3.03%
Largest Contig: 178.3 KB
Main genome scaffold total: 67
Main genome contig total: 71
Main genome scaffold sequence total: 3.4 MB
Main genome contig sequence total: 3.4 MB (-> 0.0% gap)
Main genome scaffold N/L50: 13/89.6 KB
Main genome contig N/L50: 13/86.4 KB
Number of scaffolds > 50 KB: 28
% main genome in scaffolds > 50 KB: 81.1%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 67 71 3,387,070 3,385,761 99.96%
1 kb 67 71 3,387,070 3,385,761 99.96%
2.5 kb 63 67 3,380,604 3,379,295 99.96%
5 kb 59 63 3,364,029 3,362,720 99.96%
10 kb 53 57 3,317,531 3,316,222 99.96%
25 kb 36 40 3,035,007 3,033,698 99.96%
50 kb 28 31 2,747,568 2,747,074 99.98%
100 kb 12 14 1,644,856 1,644,547 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 Mar 29 15:09:10 PDT 2013 By Alexander Spunde- [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 |
