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QD/SD JGI ISOLATES QC AND ASSEMBLY REPORT -
1) RAW DATA:
LibraryName NumReads ReadType ReadType FileName
LIB 34941350 2x150 Illumina Std PE (cassava 1.8) 6812.2.55163.ACAGTG.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: 34941350 (100%)
Artifact reads removed: 17302 (0.0%)
Total reads removed: 17302 (0.0%)
Total reads remaining: 34924048 (100.0%)
3) ILLUMINA STD PE READ IDENTIFICATION STATS
This step identifies contaminants but does not remove them from the dataset.
Total input reads: 34941350 (100%)
Num contam reads identified: 702 (0.0%)
- Ralstonia 694 0.00%
- Delftia 6 0.00%
- Cupriavidus 2 0.00%
4) ASSEMBLY STATS:
a) Velvet assembly:
Assembly stats of the Velvet assembly.
Avg GC Content: 30.69 +/- 3.26%
Largest Contig: 7.6 KB
Main genome scaffold total: 647
Main genome contig total: 647
Main genome scaffold sequence total: 962.5 KB
Main genome contig sequence total: 962.5 KB (-> 0.0% gap)
Main genome scaffold N/L50: 145/2.1 KB
Main genome contig N/L50: 145/2.1 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 647 647 962,514 962,514 100.00%
1 kb 325 325 740,559 740,559 100.00%
2.5 kb 106 106 394,554 394,554 100.00%
5 kb 15 15 90,515 90,515 100.00%
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 artifacts.
Avg GC Content: 30.58 +/- 3.11%
Largest Contig: 6.3 KB
Main genome scaffold total: 106
Main genome contig total: 106
Main genome scaffold sequence total: 218.7 KB
Main genome contig sequence total: 218.7 KB (-> 0.0% gap)
Main genome scaffold N/L50: 33/2.3 KB
Main genome contig N/L50: 33/2.3 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 106 106 218,672 218,662 100.00%
1 kb 106 106 218,672 218,662 100.00%
2.5 kb 28 28 98,259 98,249 99.99%
5 kb 3 3 17,856 17,856 100.00%
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
Velveth params: 63 -shortPaired
Velvetg params: -very_clean yes -exportFiltered yes -min_contig_lgth 500 -scaffolding no -exp_cov 200
c) 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,,,1000,100,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:
Wed May 8 11:10:06 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).
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