Deferribacteres bacterium SCGC AAA007-K08
Seq. Project name:
Deferribacteres bacterium SCGC AAA007-K08 ( Project ID: 1014044 )
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
Related Projects:
FD 1014043; SP 1014044; AP 1092670
Release Date:
2017-12-13
Organism
Genus/species/strain/isolate: Deferribacteres bacterium SCGC AAA007-K08 / SCGC AAA007-K08 / SCGC AAA007-K08
GOLD ID: Gp0033589
Data Submission
NCBI BioProject ID: 190787
NCBI Tax ID: 75994
SRA accession:
  • SRP025274 (2013-06-11)
Contacts
JGI: [email protected]
Request DNA:
Ramunas Stepanauskas <[email protected]>
General Information
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1014044 unclassified Acidobacteria (miscellaneous) 1) RAW DATA: LibraryName NumReads ReadType ReadType FileName LIB 31863260 2x157 Illumina Std PE (cassava 1.8) 6669.2.51254.GATCAG.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: 31863260 (100%) Num contam reads removed: 8 (0.0%) - human_chr1 1 0.00% - human_chr16 1 0.00% - human_chr11 1 0.00% - human_chr6 1 0.00% Artifact reads removed: 432614 (1.4%) Normalized reads removed: 31169148 (97.8%) Total reads removed: 31601770 (99.2%) Total reads remaining: 261490 (0.8%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 31863260 (100%) Num contam reads identified: 0 (0.0%) 4) ASSEMBLY STATS: a) IDBA-UD: Avg GC Content: 53.62 +/- 5.95% Largest Contig: 30.6 KB Main genome scaffold total: 574 Main genome contig total: 574 Main genome scaffold sequence total: 1.4 MB Main genome contig sequence total: 1.4 MB (-> 0.0% gap) Main genome scaffold N/L50: 57/6.9 KB Main genome contig N/L50: 57/6.9 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 574 574 1,446,069 1,446,069 100.00% 1 kb 259 259 1,283,080 1,283,080 100.00% 2.5 kb 138 138 1,091,795 1,091,795 100.00% 5 kb 85 85 894,927 894,927 100.00% 10 kb 32 32 526,678 526,678 100.00% 25 kb 3 3 90,203 90,203 100.00% 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: 54.51 +/- 3.26% Largest Contig: 104.3 KB Main genome scaffold total: 86 Main genome contig total: 87 Main genome scaffold sequence total: 1.2 MB Main genome contig sequence total: 1.2 MB (-> 0.0% gap) Main genome scaffold N/L50: 16/22.4 KB Main genome contig N/L50: 16/22.4 KB Number of scaffolds > 50 KB: 3 % main genome in scaffolds > 50 KB: 18.1% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 86 87 1,155,325 1,155,000 99.97% 1 kb 86 87 1,155,325 1,155,000 99.97% 2.5 kb 74 75 1,129,642 1,129,317 99.97% 5 kb 60 60 1,082,307 1,082,287 100.00% 10 kb 38 38 924,256 924,236 100.00% 25 kb 11 11 479,080 479,080 100.00% 50 kb 3 3 209,325 209,325 100.00% 100 kb 1 1 104,255 104,255 100.00% 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 09:59:46 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
This portal belongs to the following groups
## Name Type
1 Deferribacteres