Seq. Project name:
Deferribacteres bacterium SCGC AAA001-I23
( Project ID: 1014038 )
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: | Deferribacteres bacterium SCGC AAA001-I23 / SCGC AAA001-I23 / SCGC AAA001-I23 |
| GOLD ID: | Gp0033592 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Ramunas Stepanauskas <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1014038
unclassified Acidobacteria (miscellaneous)
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 25893402 2x157 Illumina Std PE (cassava 1.8) 6669.2.51254.TTAGGC.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: 25893402 (100%)
Num contam reads removed: 32564 (0.1%)
- human_chr7 16263 0.06%
- human_chrX 156 0.00%
- human_chr11 96 0.00%
- human_chr14 93 0.00%
- human_chr12 77 0.00%
- human_chr17 72 0.00%
- human_chr21 56 0.00%
- human_chr16 47 0.00%
- human_chr19 46 0.00%
- human_chr13 33 0.00%
- human_chr15 18 0.00%
- human_chr10 16 0.00%
- human_chr18 12 0.00%
- human_chr20 9 0.00%
- human_chr5 8 0.00%
- human_chr22 6 0.00%
- human_chr1 5 0.00%
- human_chr3 3 0.00%
- human_chr6 2 0.00%
Artifact reads removed: 801398 (3.1%)
Normalized reads removed: 24808668 (95.8%)
Total reads removed: 25642630 (99.0%)
Total reads remaining: 250772 (1.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 25893402 (100%)
Num contam reads identified: 6 (0.0%)
- Escherichia 2 0.00%
- Delftia 2 0.00%
- Pseudomonas 2 0.00%
4) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 48.30 +/- 6.57%
Largest Contig: 16.4 KB
Main genome scaffold total: 628
Main genome contig total: 628
Main genome scaffold sequence total: 1.2 MB
Main genome contig sequence total: 1.2 MB (-> 0.0% gap)
Main genome scaffold N/L50: 91/4.0 KB
Main genome contig N/L50: 91/4.0 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 628 628 1,245,605 1,245,605 100.00%
1 kb 312 312 1,078,473 1,078,473 100.00%
2.5 kb 160 160 839,795 839,795 100.00%
5 kb 64 64 507,767 507,767 100.00%
10 kb 14 14 170,809 170,809 100.00%
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: 48.57 +/- 5.53%
Largest Contig: 38.0 KB
Main genome scaffold total: 137
Main genome contig total: 138
Main genome scaffold sequence total: 962.2 KB
Main genome contig sequence total: 961.9 KB (-> 0.0% gap)
Main genome scaffold N/L50: 32/10.0 KB
Main genome contig N/L50: 33/10.0 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 137 138 962,164 961,899 99.97%
1 kb 137 138 962,164 961,899 99.97%
2.5 kb 117 118 918,363 918,098 99.97%
5 kb 73 74 770,198 769,933 99.97%
10 kb 32 33 482,627 482,362 99.95%
25 kb 2 2 66,149 66,149 100.00%
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 09:51:29 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 2.1.2.1).
|
| 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 | Deferribacteres |
