Seq. Project name:
Deltaproteobacteria bacterium SCGC AAA003-F15
( Project ID: 1015824 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
Dark ocean microbial single cell genomics
(Proposal ID: 620)
Project PI:
User Program:
CSP
Program Year:
2012
Scientific Program:
Microbial
Release Date:
2017-12-13
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Deltaproteobacteria bacterium SCGC AAA003-F15 / SCGC AAA003-F15 / SCGC AAA003-F15 |
| GOLD ID: | Gp0033498 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Ramunas Stepanauskas <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1015824
Deltaproteobacteria bacterium SCGC AAA003-F15
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
NPBX 26874434 2x150 Illumina Std PE (cassava 1.8) 6668.1.51104.GAGTGG.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: 26874434 (100%)
Num contam reads removed: 24202 (0.1%)
- human_chr11 11322 0.04%
- human_chr2 400 0.00%
- human_chr4 130 0.00%
- human_chr12 106 0.00%
- human_chr1 98 0.00%
- human_chr14 17 0.00%
- human_chr6 17 0.00%
- human_chr7 13 0.00%
- human_chr17 9 0.00%
- human_chr10 8 0.00%
- human_chr20 8 0.00%
- human_chr13 7 0.00%
- human_chrX 7 0.00%
- human_chr18 6 0.00%
- human_chr5 4 0.00%
- human_chr9 3 0.00%
- human_chr16 3 0.00%
- human_chr19 2 0.00%
- human_chr3 1 0.00%
- human_chr8 1 0.00%
- human_chr15 1 0.00%
- human_chrY 1 0.00%
Artifact reads removed: 4 (0.0%)
Normalized reads removed: 26575688 (98.9%)
Total reads removed: 26599894 (99.0%)
Total reads remaining: 274540 (1.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 26874434 (100%)
Num contam reads identified: 8 (0.0%)
- Escherichia 2 0.00%
- Delftia 2 0.00%
- Pseudomonas 2 0.00%
- Ralstonia 2 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 39.46 +/- 5.10%
Largest Contig: 28.5 KB
Main genome scaffold total: 666
Main genome contig total: 666
Main genome scaffold sequence total: 1.4 MB
Main genome contig sequence total: 1.4 MB (-> 0.0% gap)
Main genome scaffold N/L50: 84/4.1 KB
Main genome contig N/L50: 84/4.1 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 666 666 1,364,882 1,364,882 100.00%
1 kb 322 322 1,189,030 1,189,030 100.00%
2.5 kb 155 155 918,994 918,994 100.00%
5 kb 69 69 615,293 615,293 100.00%
10 kb 17 17 264,856 264,856 100.00%
25 kb 1 1 28,492 28,492 100.00%
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: 41.33 +/- 3.13%
Largest Contig: 53.1 KB
Main genome scaffold total: 139
Main genome contig total: 139
Main genome scaffold sequence total: 1.1 MB
Main genome contig sequence total: 1.1 MB (-> 0.0% gap)
Main genome scaffold N/L50: 28/10.8 KB
Main genome contig N/L50: 28/10.8 KB
Number of scaffolds > 50 KB: 1
% main genome in scaffolds > 50 KB: 5.0%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 139 139 1,057,534 1,057,534 100.00%
1 kb 139 139 1,057,534 1,057,534 100.00%
2.5 kb 115 115 1,006,608 1,006,608 100.00%
5 kb 69 69 846,782 846,782 100.00%
10 kb 33 33 583,248 583,248 100.00%
25 kb 4 4 151,936 151,936 100.00%
50 kb 1 1 53,083 53,083 100.00%
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:
02/22/2013
9) AUTHORS:
For additional information, please contact:
NAME_OF_ANALYST - [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 | Deltaproteobacteria |
