Seq. Project name:
Ensifer sp. JGI 0001036-M18
( Project ID: 1017909 )
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:
2011
Scientific Program:
Microbial
Release Date:
2016-09-24
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Ensifer / Ensifer sp. JGI 0001036-M18 / JGI 0001036-M18 / |
| GOLD ID: | Gp0035302 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Scott Clingenpeel <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1017909
uncultured Sinorhizobium sp.
1) RAW DATA:
LibraryName NumReads RunType ReadType FileName
LIB 16880066 2x150 Illumina Std PE (cassava 1.8) 6920.2.57855.TACAGC.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: 16880066 (100%)
Num contam reads removed: 382 (0.0%)
- human_chr20 171 0.00%
- human_chr2 5 0.00%
- human_chr15 3 0.00%
- human_chr1 2 0.00%
- human_chr16 2 0.00%
- human_chr9 2 0.00%
- human_chr13 1 0.00%
- human_chr18 1 0.00%
- human_chr5 1 0.00%
- human_chr21 1 0.00%
- human_chr10 1 0.00%
- human_chrX 1 0.00%
- human_chr3 1 0.00%
- human_chr4 1 0.00%
Artifact reads removed: 190952 (1.1%)
Normalized reads removed: 16560872 (98.1%)
Total reads removed: 16752206 (99.2%)
Total reads remaining: 127860 (0.8%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 16880066 (100%)
Num contam reads identified: 4 (0.0%)
- Cupriavidus 4 0.00%
4) NCBI SCREENING STATS
This step identifies potential contaminants screened by NCBI for submission.
Query Subject AlignLength PctId
scaffold00024.1 UVEC:J01749 2692 99.96
scaffold00031.1 CVEC:pWE15A 1291 99.92
5) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 59.86 +/- 4.80%
Largest Contig: 40.5 KB
Main genome scaffold total: 209
Main genome contig total: 209
Main genome scaffold sequence total: 557.0 KB
Main genome contig sequence total: 557.0 KB (-> 0.0% gap)
Main genome scaffold N/L50: 16/10.9 KB
Main genome contig N/L50: 16/10.9 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 209 209 557,031 557,031 100.00%
1 kb 94 94 497,038 497,038 100.00%
2.5 kb 47 47 428,941 428,941 100.00%
5 kb 25 25 349,898 349,898 100.00%
10 kb 16 16 282,569 282,569 100.00%
25 kb 3 3 104,196 104,196 100.00%
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 contamination, artifacts and normalized.
Avg GC Content: 58.44 +/- 6.03%
Largest Contig: 50.8 KB
Main genome scaffold total: 33
Main genome contig total: 33
Main genome scaffold sequence total: 452.9 KB
Main genome contig sequence total: 452.9 KB (-> 0.0% gap)
Main genome scaffold N/L50: 7/25.5 KB
Main genome contig N/L50: 7/25.5 KB
Number of scaffolds > 50 KB: 1
% main genome in scaffolds > 50 KB: 11.2%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 33 33 452,924 452,924 100.00%
1 kb 33 33 452,924 452,924 100.00%
2.5 kb 27 27 440,322 440,322 100.00%
5 kb 21 21 421,209 421,209 100.00%
10 kb 17 17 393,043 393,043 100.00%
25 kb 7 7 242,055 242,055 100.00%
50 kb 1 1 50,837 50,837 100.00%
6) 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
7) 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 velvet simulated read pairs (step 5) and the contam+artifact+normalized filtered data.
8) ASSEMBLERS USED:
IDBA-UD, AllpathsLG
9) RELEASE DATE:
Tue May 14 15:32:49 PDT 2013 By Alexander Spunde- [email protected]
10) 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 | Alphaproteobacteria | |
| 2 | Proteobacteria |
