Seq. Project name:
Delftia sp. JGI 001020-O15
( Project ID: 1011477 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
Rhizosphere Grand Challenge Single Cell Sequencing
(Proposal ID: 939)
Project PI:
User Program:
Grand Challenge
Program Year:
2009
Scientific Program:
Microbial
Release Date:
2023-02-24
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Delftia / Delftia sp. JGI 0001020-O15 / JGI 0001020-O15 / |
| GOLD ID: | Gp0024711 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Susannah Tringe <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1011477
Delftia sp. JGI 001020-O15
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
HNYS 23169428 2x150 Illumina Std PE (cassava 1.8) 6386.2.43679.CCGTCC.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: 23169428 (100%)
Num contam reads removed: 4 (0.0%)
- human_chr18 1 0.00%
- human_chr15 1 0.00%
Artifact reads removed: 532974 (2.3%)
Normalized reads removed: 22551012 (97.3%)
Total reads removed: 23083990 (99.6%)
Total reads remaining: 85438 (0.4%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 23169428 (100%)
Num contam reads identified: 3645792 (15.7%)
- Delftia 3610150 15.58%
- Ralstonia 35134 0.15%
- Escherichia 386 0.00%
- Shigella 98 0.00%
- Cupriavidus 12 0.00%
- Pseudomonas 12 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 53.43 +/- 10.91%
Largest Contig: 17.7 KB
Main genome scaffold total: 340
Main genome contig total: 340
Main genome scaffold sequence total: 515.8 KB
Main genome contig sequence total: 515.8 KB (-> 0.0% gap)
Main genome scaffold N/L50: 40/3.3 KB
Main genome contig N/L50: 40/3.3 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 340 340 515,812 515,812 100.00%
1 kb 118 118 399,227 399,227 100.00%
2.5 kb 54 54 300,709 300,709 100.00%
5 kb 21 21 182,852 182,852 100.00%
10 kb 4 4 52,842 52,842 100.00%
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: 52.08 +/- 11.68%
Largest Contig: 28.6 KB
Main genome scaffold total: 54
Main genome contig total: 54
Main genome scaffold sequence total: 376.0 KB
Main genome contig sequence total: 376.0 KB (-> 0.0% gap)
Main genome scaffold N/L50: 12/9.5 KB
Main genome contig N/L50: 12/9.5 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 54 54 376,027 376,027 100.00%
1 kb 54 54 376,027 376,027 100.00%
2.5 kb 42 42 356,020 356,020 100.00%
5 kb 27 27 305,862 305,862 100.00%
10 kb 11 11 182,603 182,603 100.00%
25 kb 2 2 57,056 57,056 100.00%
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,,,1000,100,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:
01/28/2013
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 | Betaproteobacteria | |
| 2 | Proteobacteria |
