Seq. Project name:
Lentisphaerae bacterium SCGC AAA283-D08
( Project ID: 1014125 )
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
Genome Portal:
2522572186
Release Date:
2017-12-13
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Lentisphaerae bacterium SCGC AAA283-D08 / SCGC AAA283-D08 / SCGC AAA283-D08 |
| GOLD ID: | Gp0033622 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Ramunas Stepanauskas <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1014125
unclassified Lentisphaerae (miscellaneous)
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
NPAB 23222414 2x150 Illumina Std PE (cassava 1.8) 6668.1.51104.GTGGCC.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: 23222414 (100%)
Num contam reads removed: 14 (0.0%)
- human_chr2 6 0.00%
- human_chr11 1 0.00%
Artifact reads removed: 2 (0.0%)
Normalized reads removed: 23157364 (99.7%)
Total reads removed: 23157380 (99.7%)
Total reads remaining: 65034 (0.3%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 23222414 (100%)
Num contam reads identified: 4 (0.0%)
- Escherichia 2 0.00%
- Delftia 2 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 42.45 +/- 7.00%
Largest Contig: 20.4 KB
Main genome scaffold total: 283
Main genome contig total: 283
Main genome scaffold sequence total: 464.1 KB
Main genome contig sequence total: 464.1 KB (-> 0.0% gap)
Main genome scaffold N/L50: 28/4.4 KB
Main genome contig N/L50: 28/4.4 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 283 283 464,139 464,139 100.00%
1 kb 100 100 372,366 372,366 100.00%
2.5 kb 46 46 292,810 292,810 100.00%
5 kb 22 22 206,083 206,083 100.00%
10 kb 6 6 88,970 88,970 100.00%
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: 42.97 +/- 4.26%
Largest Contig: 39.7 KB
Main genome scaffold total: 38
Main genome contig total: 38
Main genome scaffold sequence total: 327.0 KB
Main genome contig sequence total: 327.0 KB (-> 0.0% gap)
Main genome scaffold N/L50: 9/11.4 KB
Main genome contig N/L50: 9/11.4 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 38 38 327,034 326,987 99.99%
1 kb 38 38 327,034 326,987 99.99%
2.5 kb 35 35 320,389 320,342 99.99%
5 kb 24 24 282,935 282,888 99.98%
10 kb 11 11 188,928 188,906 99.99%
25 kb 1 1 39,704 39,694 99.97%
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:
02/21/2013
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 | Lentisphaerae |
