Seq. Project name:
Actinobacteria bacterium SCGC AAA292-A19
( Project ID: 1015815 )
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: | Actinobacteria bacterium SCGC AAA292-A19 / SCGC AAA292-A19 / SCGC AAA292-A19 |
| GOLD ID: | Gp0033582 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Ramunas Stepanauskas <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1015815
unclassified Actinobacteria (miscellaneous)
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
NPBZ 23089096 2x157 Illumina Std PE (cassava 1.8) 6669.2.51254.TGACCA.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: 23089096 (100%)
Num contam reads removed: 10 (0.0%)
- human_chr16 1 0.00%
- human_chr2 1 0.00%
- human_chr11 1 0.00%
- human_chr4 1 0.00%
- human_chr10 1 0.00%
- human_chr7 1 0.00%
Artifact reads removed: 10 (0.0%)
Normalized reads removed: 22897852 (99.2%)
Total reads removed: 22897872 (99.2%)
Total reads remaining: 191224 (0.8%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 23089096 (100%)
Num contam reads identified: 4 (0.0%)
- Pseudomonas 4 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 32.24 +/- 10.12%
Largest Contig: 32.8 KB
Main genome scaffold total: 333
Main genome contig total: 333
Main genome scaffold sequence total: 938.7 KB
Main genome contig sequence total: 938.7 KB (-> 0.0% gap)
Main genome scaffold N/L50: 42/6.0 KB
Main genome contig N/L50: 42/6.0 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 333 333 938,725 938,725 100.00%
1 kb 191 191 867,194 867,194 100.00%
2.5 kb 111 111 741,350 741,350 100.00%
5 kb 54 54 537,774 537,774 100.00%
10 kb 16 16 273,174 273,174 100.00%
25 kb 1 1 32,846 32,846 100.00%
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: 29.54 +/- 6.52%
Largest Contig: 55.4 KB
Main genome scaffold total: 70
Main genome contig total: 70
Main genome scaffold sequence total: 817.7 KB
Main genome contig sequence total: 817.7 KB (-> 0.0% gap)
Main genome scaffold N/L50: 14/18.9 KB
Main genome contig N/L50: 14/18.9 KB
Number of scaffolds > 50 KB: 1
% main genome in scaffolds > 50 KB: 6.8%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 70 70 817,718 817,718 100.00%
1 kb 70 70 817,718 817,718 100.00%
2.5 kb 67 67 811,312 811,312 100.00%
5 kb 47 47 743,876 743,876 100.00%
10 kb 27 27 600,496 600,496 100.00%
25 kb 9 9 315,146 315,146 100.00%
50 kb 1 1 55,374 55,374 100.00%
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:
Thu Apr 18 09:43:19 PDT 2013 By Alexander Spunde- [email protected]
9) 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).
|
| 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 |
