Seq. Project name:
Veillonellaceae bacterium JGI Feb_L1D1C1_F7
( Project ID: 1022599 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
Microbial community impact on carbon sequestration in managed wetland "carbon farming"
(Proposal ID: 368)
Project PI:
User Program:
CSP
Program Year:
2011
Scientific Program:
Microbial
Release Date:
2016-09-01
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Veillonellaceae bacterium JGI Feb_L1D1C1_F7 / JGI Feb_L1D1C1_F7 / |
| GOLD ID: | Gp0040573 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Susannah Tringe <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1022599
unclassified Veillonellaceae
1) RAW DATA:
LibraryName NumReads RunType ReadType FileName Platform Model
PGYB 33812518 2x150 Illumina Std PE (cassava 1.8) 7275.5.65882.GTGAAA.fastq Illumina HiSeq-2000
2) ILLUMINA STD PE READ FILTERING STATS:
Pairs of matching reads were removed from the dataset.
Total input reads: 33812518 (100%)
Num contam reads removed: 32 (0.0%)
- human_chr18 6 0.00%
- human_chr4 6 0.00%
- human_chrX 4 0.00%
- human_chr7 4 0.00%
- human_chr9 4 0.00%
- human_chr21 2 0.00%
- human_chr3 2 0.00%
- human_chr20 2 0.00%
- human_chr12 2 0.00%
- human_chr6 2 0.00%
Artifact reads removed: 27918 (0.1%)
Subsampled reads removed: 13784568 (40.8%)
Total reads removed: 13812518 (40.9%)
Total reads remaining: 20000000 (59.1%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 33812518 (100%)
Num contam reads identified: 62 (0.0%)
- Pseudomonas 60 0.00%
- Ralstonia 2 0.00%
4) NCBI SCREENING STATS
This step identifies potential contaminants screened by NCBI for submission.
** No potential contaminants found.
5) ASSEMBLY STATS:
a) SPAdes assembly:
Assembly stats of the SPAdes assembly.
Estimated Genome Recovery using Single-copy Gene Analysis:
bacteria HMM: 12.79%
archaea HMM: 6.17%
Avg GC Content: 38.46 +/- 3.87%
Largest Contig: 19.0 KB
Main genome scaffold total: 196
Main genome contig total: 196
Main genome scaffold sequence total: 1.1 MB
Main genome contig sequence total: 1.1 MB (-> 0.0% gap)
Main genome scaffold N/L50: 52/7.5 KB
Main genome contig N/L50: 52/7.5 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 196 196 1,135,103 1,135,070 100.00%
1 kb 196 196 1,135,103 1,135,070 100.00%
2.5 kb 160 160 1,054,654 1,054,632 100.00%
5 kb 86 86 788,144 788,139 100.00%
10 kb 26 26 355,952 355,952 100.00%
6) KEY PIPELINE CMDS:
a) SPAdes assembly step:
SPAdes params: --sc --careful -m 40 --12
7) WORKFLOW STEPS:
1. Removed contamination (human contaminants).
2. Removed illumina artifacts (synthetic oligos used in the laboratory).
3. Created SPAdes assembly of the contam+artifact filtered data.
8) ASSEMBLERS USED:
SPAdes (v.)
9) ASSESSED GENOME PROJECT STANDARD:
Standard Draft
10) RELEASE DATE:
Wed Sep 4 14:56:45 PDT 2013 By Alexander Spunde- [email protected]
11) 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 2.2.2).
|
| 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 | Environmental | |
| 2 | Firmicutes |
