Seq. Project name:
Bacteroidetes bacterium JGI 0002005-G08
( Project ID: 1017032 )
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: | Bacteroidetes bacterium JGI 0002005-G08 / JGI 0002005-G08 / |
| GOLD ID: | Gp0035351 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Alison Murray <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1017032
unclassified Bacteroidetes (miscellaneous)
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 32600052 2x150 Illumina Std PE (cassava 1.8) 6787.4.54588.ATCACG.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: 32600052 (100%)
Num contam reads removed: 46 (0.0%)
- human_chr2 4 0.00%
- human_chr12 3 0.00%
- human_chr15 3 0.00%
- human_chr1 2 0.00%
- human_chrX 2 0.00%
- human_chr3 2 0.00%
- human_chr13 1 0.00%
- human_chr19 1 0.00%
- human_chr7 1 0.00%
- human_chr9 1 0.00%
- human_chr8 1 0.00%
- human_chr6 1 0.00%
- human_chr4 1 0.00%
Artifact reads removed: 97824 (0.3%)
Normalized reads removed: 32377548 (99.3%)
Total reads removed: 32475418 (99.6%)
Total reads remaining: 124634 (0.4%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 32600052 (100%)
Num contam reads identified: 772 (0.0%)
- Ralstonia 698 0.00%
- Delftia 62 0.00%
- Pseudomonas 8 0.00%
- Cupriavidus 2 0.00%
- Shigella 2 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 33.61 +/- 4.91%
Largest Contig: 5.8 KB
Main genome scaffold total: 830
Main genome contig total: 830
Main genome scaffold sequence total: 662.6 KB
Main genome contig sequence total: 662.6 KB (-> 0.0% gap)
Main genome scaffold N/L50: 185/1.1 KB
Main genome contig N/L50: 185/1.1 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 830 830 662,570 662,570 100.00%
1 kb 211 211 358,645 358,645 100.00%
2.5 kb 26 26 83,276 83,276 100.00%
5 kb 2 2 11,017 11,017 100.00%
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: 34.05 +/- 3.31%
Largest Contig: 7.3 KB
Main genome scaffold total: 115
Main genome contig total: 115
Main genome scaffold sequence total: 306.4 KB
Main genome contig sequence total: 306.4 KB (-> 0.0% gap)
Main genome scaffold N/L50: 41/3.0 KB
Main genome contig N/L50: 41/3.0 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 115 115 306,353 306,353 100.00%
1 kb 115 115 306,353 306,353 100.00%
2.5 kb 58 58 200,141 200,141 100.00%
5 kb 4 4 23,249 23,249 100.00%
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 10:19:42 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 | Bacteroidetes |
