Seq. Project name:
Ignavibacteriaceae bacterium SCGC AB-674-E22
( Project ID: 1018675 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
Enigmatic life underneath us: genomic analysis of deep subsurface microorganisms
(Proposal ID: 987)
Project PI:
User Program:
CSP
Program Year:
2013
Scientific Program:
Microbial
Release Date:
2023-02-24
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Ignavibacteriaceae bacterium SCGC AB-674-E22 / SCGC AB-674-E22 / |
| GOLD ID: | Gp0036401 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Ramunas Stepanauskas <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1018675
uncultured Ignavibacteriaceae bacterium
1) RAW DATA:
LibraryName NumReads RunType ReadType FileName Platform Model
PUCP 28693398 2x150 Illumina Std PE (cassava 1.8) 7001.5.59507.ATGTCA.fastq Illumina HiSeq
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: 28693398 (100%)
Num contam reads removed: 2 (0.0%)
- human_chr11 1 0.00%
- human_chr4 1 0.00%
Artifact reads removed: 126650 (0.4%)
Normalized reads removed: 28177348 (98.2%)
Total reads removed: 28304000 (98.6%)
Total reads remaining: 389398 (1.4%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 28693398 (100%)
Num contam reads identified: 0 (0.0%)
4) NCBI SCREENING STATS
This step identifies potential contaminants screened by NCBI for submission.
** No potential contaminants found.
5) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 35.65 +/- 3.61%
Largest Contig: 21.9 KB
Main genome scaffold total: 792
Main genome contig total: 792
Main genome scaffold sequence total: 1.7 MB
Main genome contig sequence total: 1.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 102/4.4 KB
Main genome contig N/L50: 102/4.4 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 792 792 1,676,940 1,676,940 100.00%
1 kb 397 397 1,477,466 1,477,466 100.00%
2.5 kb 205 205 1,173,780 1,173,780 100.00%
5 kb 90 90 783,787 783,787 100.00%
10 kb 28 28 361,633 361,633 100.00%
b) Allpaths + Velvet simulated read pairs:
Assembly stats of the ALLPATHS assembly. The input contains simulated
1-3 kb read pairs created from the Velvet assembly and reads that
have been filtered for contamination, artifacts and normalized.
Avg GC Content: 35.46 +/- 2.46%
Largest Contig: 62.2 KB
Main genome scaffold total: 160
Main genome contig total: 162
Main genome scaffold sequence total: 1.3 MB
Main genome contig sequence total: 1.3 MB (-> 0.1% gap)
Main genome scaffold N/L50: 34/11.7 KB
Main genome contig N/L50: 34/11.7 KB
Number of scaffolds > 50 KB: 1
% main genome in scaffolds > 50 KB: 4.7%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 160 162 1,327,742 1,325,807 99.85%
1 kb 160 162 1,327,742 1,325,807 99.85%
2.5 kb 136 138 1,277,642 1,275,707 99.85%
5 kb 86 88 1,108,081 1,106,146 99.83%
10 kb 50 52 847,596 845,661 99.77%
25 kb 5 5 183,522 183,502 99.99%
50 kb 1 1 62,243 62,243 100.00%
6) 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
7) 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 velvet simulated read pairs (step 5) and the contam+artifact+normalized filtered data.
8) ASSEMBLERS USED:
IDBA-UD, AllpathsLG
9) RELEASE DATE:
Fri Jul 19 14:30:11 PDT 2013 By Alexander Spunde- [email protected]
10) 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).
-- Additional Note By Alexander Spunde @ Fri Jul 19 14:30:11 PDT 2013 --
Note: no 16S in the assembly; although acceptable for SAG, makes confirmation of target genome less certain.
|
| 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 | Environmental |
