Seq. Project name:
Microlunatus sp. JGI 0001013-N15
( Project ID: 1017864 )
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: | Microlunatus / Microlunatus sp. / JGI 0001013-N15 / |
| GOLD ID: | Gp0035257 |
| Contacts | |
|---|---|
| JGI: | [email protected] |
| Request DNA: | Scott Clingenpeel <[email protected]> |
| General Information | |
|---|---|
|
QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT -
1017864
uncultured Microlunatus sp.
1) RAW DATA:
LibraryName NumReads RunType ReadType FileName
LIB 15735676 2x150 Illumina Std PE (cassava 1.8) 6920.4.57857.CAAAAG.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: 15735676 (100%)
Num contam reads removed: 8460 (0.1%)
- human_chr4 3151 0.02%
- human_chr3 1038 0.01%
- human_chrX 375 0.00%
- human_chr10 215 0.00%
- human_chr11 203 0.00%
- human_chr18 173 0.00%
- human_chr12 159 0.00%
- human_chr14 151 0.00%
- human_chr19 106 0.00%
- human_chr17 84 0.00%
- human_chr13 48 0.00%
- human_chr20 48 0.00%
- human_chr15 38 0.00%
- human_chr22 23 0.00%
- human_chr6 18 0.00%
- human_chr21 13 0.00%
- human_chr16 11 0.00%
- human_chr9 9 0.00%
- human_chr1 4 0.00%
- human_chr2 4 0.00%
- human_chr8 3 0.00%
- human_chr5 3 0.00%
- human_chrY 3 0.00%
Artifact reads removed: 1600340 (10.2%)
Normalized reads removed: 13950312 (88.7%)
Total reads removed: 15559112 (98.9%)
Total reads remaining: 176564 (1.1%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 15735676 (100%)
Num contam reads identified: 33914 (0.2%)
- Escherichia 28250 0.18%
- Shigella 5620 0.04%
- Delftia 44 0.00%
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: 55.25 +/- 11.38%
Largest Contig: 32.0 KB
Main genome scaffold total: 275
Main genome contig total: 275
Main genome scaffold sequence total: 513.8 KB
Main genome contig sequence total: 513.8 KB (-> 0.0% gap)
Main genome scaffold N/L50: 24/4.9 KB
Main genome contig N/L50: 24/4.9 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 275 275 513,787 513,787 100.00%
1 kb 102 102 429,969 429,969 100.00%
2.5 kb 52 52 353,973 353,973 100.00%
5 kb 23 23 253,562 253,562 100.00%
10 kb 6 6 138,739 138,739 100.00%
25 kb 3 3 90,735 90,735 100.00%
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: 58.86 +/- 12.05%
Largest Contig: 38.2 KB
Main genome scaffold total: 38
Main genome contig total: 38
Main genome scaffold sequence total: 356.8 KB
Main genome contig sequence total: 356.8 KB (-> 0.0% gap)
Main genome scaffold N/L50: 7/13.9 KB
Main genome contig N/L50: 7/13.9 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 38 38 356,811 356,811 100.00%
1 kb 38 38 356,811 356,811 100.00%
2.5 kb 31 31 341,477 341,477 100.00%
5 kb 23 23 312,389 312,389 100.00%
10 kb 9 9 208,930 208,930 100.00%
25 kb 4 4 140,184 140,184 100.00%
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 11:06:33 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 | Actinobacteria |
