Seq. Project name:
Caulobacter sp. JGI 0001041-J05
( Project ID: 1017843 )
Product:
Microbial Minimal Draft, Single Cell
Proposal Name:
Rhizosphere Grand Challenge Single Cell Sequencing
(Proposal ID: 939)
Project PI:
User Program:
Grand Challenge
Program Year:
2011
Scientific Program:
Microbial
Release Date:
2016-09-24
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Caulobacter / Caulobacter sp. / JGI 0001041-J05 / |
| GOLD ID: | Gp0025710 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Scott Clingenpeel <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1017843
uncultured Caulobacter sp.
1) RAW DATA:
LibraryName NumReads RunType ReadType FileName
LIB 21217444 2x150 Illumina Std PE (cassava 1.8) 6920.3.57856.GTTTCG.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: 21217444 (100%)
Num contam reads removed: 24476 (0.1%)
- human_chr4 12204 0.06%
- human_chrX 984 0.00%
- human_chr10 728 0.00%
- human_chr11 377 0.00%
- human_chr13 345 0.00%
- human_chr12 343 0.00%
- human_chr17 338 0.00%
- human_chr14 277 0.00%
- human_chr20 269 0.00%
- human_chr18 148 0.00%
- human_chr19 114 0.00%
- human_chr15 107 0.00%
- human_chr16 103 0.00%
- human_chr21 101 0.00%
- human_chrY 29 0.00%
- human_chr22 19 0.00%
- human_chr7 13 0.00%
- human_chr2 9 0.00%
- human_chr6 8 0.00%
- human_chr1 7 0.00%
- human_chr9 7 0.00%
- human_chr3 3 0.00%
- human_chr5 2 0.00%
Artifact reads removed: 129804 (0.6%)
Normalized reads removed: 20745108 (97.8%)
Total reads removed: 20899388 (98.5%)
Total reads remaining: 318056 (1.5%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 21217444 (100%)
Num contam reads identified: 638 (0.0%)
- Ralstonia 412 0.00%
- Escherichia 194 0.00%
- Shigella 32 0.00%
4) NCBI SCREENING STATS
This step identifies potential contaminants screened by NCBI for submission.
Query Subject AlignLength PctId
scaffold00050.1 UVEC:J01749 3660 99.95
5) ASSEMBLY STATS:
a) IDBA-UD:
Avg GC Content: 63.87 +/- 10.02%
Largest Contig: 42.2 KB
Main genome scaffold total: 601
Main genome contig total: 601
Main genome scaffold sequence total: 1.4 MB
Main genome contig sequence total: 1.4 MB (-> 0.0% gap)
Main genome scaffold N/L50: 51/7.3 KB
Main genome contig N/L50: 51/7.3 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 601 601 1,437,051 1,437,051 100.00%
1 kb 243 243 1,258,512 1,258,512 100.00%
2.5 kb 127 127 1,065,500 1,065,500 100.00%
5 kb 77 77 884,001 884,001 100.00%
10 kb 26 26 502,488 502,488 100.00%
25 kb 5 5 167,522 167,522 100.00%
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: 66.48 +/- 4.78%
Largest Contig: 54.6 KB
Main genome scaffold total: 110
Main genome contig total: 112
Main genome scaffold sequence total: 1.2 MB
Main genome contig sequence total: 1.1 MB (-> 0.1% gap)
Main genome scaffold N/L50: 21/19.5 KB
Main genome contig N/L50: 21/19.5 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 110 112 1,150,516 1,149,246 99.89%
1 kb 110 112 1,150,516 1,149,246 99.89%
2.5 kb 92 94 1,111,928 1,110,658 99.89%
5 kb 70 71 1,034,132 1,033,857 99.97%
10 kb 36 37 792,972 792,697 99.97%
25 kb 11 12 371,412 371,137 99.93%
50 kb 1 1 54,606 54,606 100.00%
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:
Thu May 23 14:20:57 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).
|
| 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 | Alphaproteobacteria | |
| 2 | Proteobacteria |
