Seq. Project name:
Gammaproteobacteria bacterium JGI 0002005-J21
( Project ID: 1017047 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
Lake Vida brine microbial community (LVBMCo) genomics and transcriptomics - a window into diversity, adaptation and processes in extreme cold
(Proposal ID: 634)
Project PI:
User Program:
CSP
Program Year:
2012
Scientific Program:
Microbial
Release Date:
2016-09-01
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Gammaproteobacteria bacterium JGI 0002005-J21 / JGI 0002005-J21 / |
| GOLD ID: | Gp0035356 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Alison Murray <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1017047
unclassified Gammaproteobacteria (miscellaneous)
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 32229080 2x150 Illumina Std PE (cassava 1.8) 6787.4.54588.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: 32229080 (100%)
Num contam reads removed: 640 (0.0%)
- human_chr2 29 0.00%
- human_chr7 28 0.00%
- human_chr5 26 0.00%
- human_chr8 22 0.00%
- human_chr11 21 0.00%
- human_chr10 21 0.00%
- human_chr4 21 0.00%
- human_chr3 18 0.00%
- human_chr6 18 0.00%
- human_chr9 17 0.00%
- human_chrX 14 0.00%
- human_chr14 13 0.00%
- human_chr1 11 0.00%
- human_chr12 11 0.00%
- human_chr21 9 0.00%
- human_chr16 8 0.00%
- human_chr20 8 0.00%
- human_chr13 7 0.00%
- human_chr18 7 0.00%
- human_chr15 6 0.00%
- human_chr22 5 0.00%
- human_chr19 5 0.00%
- human_chr17 5 0.00%
- human_chrY 1 0.00%
Artifact reads removed: 125784 (0.4%)
Normalized reads removed: 32014940 (99.3%)
Total reads removed: 32141364 (99.7%)
Total reads remaining: 87716 (0.3%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 32229080 (100%)
Num contam reads identified: 1222 (0.0%)
- Ralstonia 1204 0.00%
- Delftia 10 0.00%
- Pseudomonas 6 0.00%
- Escherichia 1 0.00%
- Shigella 1 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 46.98 +/- 8.23%
Largest Contig: 13.7 KB
Main genome scaffold total: 441
Main genome contig total: 441
Main genome scaffold sequence total: 463.6 KB
Main genome contig sequence total: 463.6 KB (-> 0.0% gap)
Main genome scaffold N/L50: 79/1.5 KB
Main genome contig N/L50: 79/1.5 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 441 441 463,622 463,622 100.00%
1 kb 147 147 314,015 314,015 100.00%
2.5 kb 24 24 127,712 127,712 100.00%
5 kb 9 9 77,488 77,488 100.00%
10 kb 3 3 35,361 35,361 100.00%
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: 47.92 +/- 7.56%
Largest Contig: 15.6 KB
Main genome scaffold total: 79
Main genome contig total: 79
Main genome scaffold sequence total: 256.5 KB
Main genome contig sequence total: 256.5 KB (-> 0.0% gap)
Main genome scaffold N/L50: 20/3.4 KB
Main genome contig N/L50: 20/3.4 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 79 79 256,522 256,522 100.00%
1 kb 79 79 256,522 256,522 100.00%
2.5 kb 34 34 171,096 171,096 100.00%
5 kb 12 12 99,424 99,424 100.00%
10 kb 4 4 47,635 47,635 100.00%
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:
Fri Apr 26 10:39:01 PDT 2013 By Kecia Duffy- [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 2.1.2.1).
|
| 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 | Gammaproteobacteria | |
| 2 | Proteobacteria |
