Seq. Project name:
Acidaminococcus intestini DSM 21505
( Project ID: 1013604 )
Product:
Microbial Minimal Draft, Isolate
Proposal Name:
Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
(Proposal ID: 733)
Project PI:
User Program:
CSP
Program Year:
2012
Scientific Program:
Microbial
Release Date:
2013-05-31
| Organism | |
|---|---|
| Genus/species/strain/isolate: | Acidaminococcus / Acidaminococcus intestini / DSM 21505 / |
| GOLD ID: | Gp0013860 |
| Contacts | |
|---|---|
| JGI: | |
| Request DNA: | Nikos Kyrpides <[email protected]> |
| General Information | |
|---|---|
|
QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1013604
Acidaminococcus intestini DSM 21505
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 11643072 2x150 Illumina Std PE (cassava 1.8) 6622.3.49215.CGTACG.fastq
2) ILLUMINA STD PE READ FILTERING STATS:
Reads were screened against synthetic oligos used in the Illumina
sequencing process. Pairs of matching reads were removed from the
dataset.
Total input reads: 11643072 (100%)
Artifact reads removed: 14 (0.0%)
Total reads removed: 14 (0.0%)
Total reads remaining: 11643058 (100.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 11643072 (100%)
Num contam reads identified: 2 (0.0%)
- Pseudomonas 2 0.00%
4) ASSEMBLY STATS:
a) Velvet assembly using VelvetOptimizer:
Assembly stats of the Velvet assembly created by the velvet
optimizer.
Avg GC Content: 49.00 +/- 3.03%
Largest Contig: 204.9 KB
Main genome scaffold total: 64
Main genome contig total: 109
Main genome scaffold sequence total: 2.3 MB
Main genome contig sequence total: 2.3 MB (-> 0.1% gap)
Main genome scaffold N/L50: 11/54.4 KB
Main genome contig N/L50: 22/38.3 KB
Number of scaffolds > 50 KB: 14
% main genome in scaffolds > 50 KB: 58.6%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 64 109 2,268,194 2,264,455 99.84%
1 kb 60 105 2,265,288 2,261,549 99.83%
2.5 kb 53 98 2,255,268 2,251,529 99.83%
5 kb 47 92 2,233,223 2,229,484 99.83%
10 kb 43 88 2,205,826 2,202,087 99.83%
25 kb 34 77 2,076,333 2,072,710 99.83%
50 kb 14 42 1,329,182 1,326,785 99.82%
100 kb 4 19 623,826 622,529 99.79%
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 artifacts.
Avg GC Content: 49.57 +/- 2.20%
Largest Contig: 205.4 KB
Main genome scaffold total: 55
Main genome contig total: 57
Main genome scaffold sequence total: 2.3 MB
Main genome contig sequence total: 2.3 MB (-> 0.2% gap)
Main genome scaffold N/L50: 11/55.0 KB
Main genome contig N/L50: 11/55.0 KB
Number of scaffolds > 50 KB: 14
% main genome in scaffolds > 50 KB: 58.5%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 55 57 2,282,467 2,278,607 99.83%
1 kb 55 57 2,282,467 2,278,607 99.83%
2.5 kb 53 55 2,279,014 2,275,154 99.83%
5 kb 48 50 2,261,386 2,257,526 99.83%
10 kb 44 46 2,237,623 2,233,763 99.83%
25 kb 34 36 2,093,267 2,089,407 99.82%
50 kb 14 15 1,334,841 1,334,176 99.95%
100 kb 4 5 625,338 624,673 99.89%
5) KEY PIPELINE CMDS:
a) Artifact removal step:
duk params: -k 22 -s 1 -c 1
b) Velvet assembly step for creating simulated read pairs:
Velvet version: 1.1.04
Velvet optimizer version: 2.1.7
Velvet optimizer params: --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500"
c) Simulated read pairing creation step:
Wgsim version: 0.3.0
Wgsim params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0
d) 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 illumina artifacts (synthetic oligos used in the laboratory).
2. Created velvet assembly of the artifact filtered data.
3. Created simulated 1-3 kb read pairs using Velvet contigs from step 2.
4. Created allpaths assembly using Velvet simulated read pairs (step 3) and the artifact filtered data.
7) ASSEMBLERS USED:
Velvet, AllpathsLG
8) RELEASE DATE:
Thu May 16 16:14:51 PDT 2013 By Hui Sun- [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 | Firmicutes | |
| 2 | Host Associated |
