Seq. Project name:
Eudoraea sp. SCGC 5353
( Project ID: 1017603 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
COGITO (Coastal Microbe Genomic & Taxonomic Observatory)
(Proposal ID: 998)
Project PI:
User Program:
CSP
Program Year:
2013
Scientific Program:
Microbial
Release Date:
2016-09-01
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Eudoraea / Eudoraea sp. SCGC 5353 / SCGC 5353 / |
| GOLD ID: | Gp0035123 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Hanno Teeling <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1017603
uncultured Eudoraea sp.
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 40149410 2x150 Illumina Std PE (cassava 1.8) 6812.2.55163.TAGCTT.fastq
2) ILLUMINA STD PE READ FILTERING STATS:
Reads were screened against human contaminants, synthetic oligos used
in the Illumina sequencing process and normalized. Pairs of matching
reads were removed from the dataset.
Total input reads: 40149410 (100%)
Num contam reads removed: 38 (0.0%)
- human_chr13 3 0.00%
- human_chr8 3 0.00%
- human_chr12 3 0.00%
- human_chr15 2 0.00%
- human_chr1 1 0.00%
- human_chr18 1 0.00%
- human_chr17 1 0.00%
- human_chr5 1 0.00%
- human_chr7 1 0.00%
- human_chr10 1 0.00%
- human_chr3 1 0.00%
- human_chr2 1 0.00%
- human_chr6 1 0.00%
Artifact reads removed: 30224 (0.1%)
Normalized reads removed: 39593760 (98.6%)
Total reads removed: 39624022 (98.7%)
Total reads remaining: 525388 (1.3%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 40149410 (100%)
Num contam reads identified: 40 (0.0%)
- Pseudomonas 36 0.00%
- Delftia 2 0.00%
- Shigella 2 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 37.60 +/- 3.51%
Largest Contig: 32.5 KB
Main genome scaffold total: 994
Main genome contig total: 994
Main genome scaffold sequence total: 2.5 MB
Main genome contig sequence total: 2.5 MB (-> 0.0% gap)
Main genome scaffold N/L50: 116/5.7 KB
Main genome contig N/L50: 116/5.7 KB
Number of scaffolds > 50 KB: 0
% main genome in scaffolds > 50 KB: 0.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 994 994 2,492,424 2,492,424 100.00%
1 kb 480 480 2,241,425 2,241,425 100.00%
2.5 kb 297 297 1,941,441 1,941,441 100.00%
5 kb 147 147 1,416,165 1,416,165 100.00%
10 kb 50 50 758,092 758,092 100.00%
25 kb 3 3 94,926 94,926 100.00%
b) Allpaths + IDBA-UD simulated read pairs:
Assembly stats of the ALLPATHS assembly. The input contains simulated
1-3 kb read pairs created from the IDBA-UD assembly and reads that
have been filtered for contamination, artifacts and normalized.
Avg GC Content: 37.52 +/- 1.96%
Largest Contig: 66.3 KB
Main genome scaffold total: 194
Main genome contig total: 194
Main genome scaffold sequence total: 2.1 MB
Main genome contig sequence total: 2.1 MB (-> 0.0% gap)
Main genome scaffold N/L50: 36/18.2 KB
Main genome contig N/L50: 36/18.2 KB
Number of scaffolds > 50 KB: 3
% main genome in scaffolds > 50 KB: 8.4%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 194 194 2,084,434 2,084,384 100.00%
1 kb 194 194 2,084,434 2,084,384 100.00%
2.5 kb 168 168 2,028,229 2,028,179 100.00%
5 kb 120 120 1,865,779 1,865,769 100.00%
10 kb 68 68 1,483,782 1,483,782 100.00%
25 kb 19 19 690,767 690,767 100.00%
50 kb 3 3 174,447 174,447 100.00%
5) KEY PIPELINE CMDS:
a) Contamination removal step:
Bwa version: 0.5.9-r16
Bwa aln params:
Bwa sampe params: -A -P -s
b) Artifact removal step:
duk params: -k 22 -s 1 -c 1
c) Normalization step:
kmernorm params: -k 21 -t 15 -c 2
d) IDBA-UD assembly step for creating simulated read pairs:
IDBA-UD version: 1.0.9
IDBA-UD params: --no_local
e) 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 contamination (human contaminants).
2. Removed illumina artifacts (synthetic oligos used in the laboratory).
3. Normalized read coverage.
4. Created IDBA-UD assembly of the contam+artifact+normalized filtered data.
5. Created simulated 1-3 kb read pairs using IDBA-UD contigs from step 4.
6. Created allpaths assembly using IDBA-UD simulated read pairs (step 5) and the contam+artifact+normalized filtered data.
7) ASSEMBLERS USED:
IDBA-UD, AllpathsLG
8) RELEASE DATE:
Mon Apr 29 11:31:29 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 2.1.2.1).
|
| 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 |
