Chris:LabNotes/Moleculo/2013/2013-5-9: Difference between revisions
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=Quick and Dirty Assembly Oncomelania Illumina contigs + moleculo data= | |||
==Background== | |||
*Dr. Zhang previously performed soapdenovo assembly on a smaller Illumina dataset, found in </media/LTS_15T/Kun_LTS/Snail/HB_species/Snail.HB.Soap.trimmed.K27.scafSeq> | |||
*We wanted to quickly check how incorporating moleculo data will help improve assembly, so we used celera assembler to do OLC assembly on contigs>100bp and all of the moleculo data (without filtering, using default settings) | |||
*Test run is found in my genemapster: </media/disk-2/cjwei/130419_Oncomelania_Illumina_Moleculo/Illumina_contigs+Moleculo_Assembly> | |||
==Procedure== | |||
*Convert Illumina contigs to fastq file format using converter utility (will create artificial fastq by assigning quality score of I to each base) -> this is required for inputting file into Celera | |||
**Go into folder <~/software/Hybrid_error_correction_assembly_software/wgs_download_2> | |||
**Use command: | |||
java convertFastaAndQualToFastq ''input_file'' > ''output_file'' | |||
*Combined both Illumina contigs fastq file + Moleculo fastq file into new file: <Illumina_contig+Moleculo.fastq> (using cat command) | |||
**It is necessary to have the correct ".fastq" file extension in order to continue forward | |||
*Create .frg file for input to celera (this is the primary input for assembly that gives general data on the read file) | |||
/media/2TB_store1/cjwei/software/Hybrid_error_correction_assembly_software/wgs_download_2/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname illumina_contigs_moleculo -reads Illumina_contig+Moleculo.fastq >Illumina_contig+Moleculo.frg | |||
**Used "-reads" option because mimic single end reads for assembly | |||
*RunCA to do assembly on combined dataset | |||
~/software/Hybrid_error_correction_assembly_software/wgs-7.0/Linux-amd64/bin/runCA -d Illumina_contig+Moleculo_assembly -p Illumina_contig+Moleculo Illumina_contig+Moleculo.frg | |||
**Without .spec file input, we are not doing correction as in normal hybrid assembly with pacbio+illumina data | |||
==Results== | |||
{| class="wikitable" | |||
|- | |||
! assembly !! n !! n:100 !! n:N50 !! min !! median !! mean !! N50 !! max !! sum | |||
|- | |||
| Illumina contig + Moleculo || 10322 || 10322 || 2812 || 1000 || 2458 || 3094 || 3682 || 17558 || 31.94e6 | |||
|- | |||
| Illumina contig || 2167043 || 2167043 || 785219 || 100 || 132 || 152 || 148 || 4661 || 329.4e6 | |||
|} | |||
*Results show a brief picture of the result of combining moleculo data with Illumina contigs. Overall, there is a dramatic increase in N50 and max contig length. However, there is a decrease in total bp assembled, probably because smaller contigs are being thrown out. | |||
*Will need to run more detailed tests to better assemble the data. Brief future plan: | |||
**Optimize assembly of Illumina reads using complete dataset | |||
**Run SEQuel on the assembled contigs to improve assembly accuracy | |||
**Hybrid assembly of Illumina contigs + Moleculo data -> will need to optimize assembly parameters for celera or explore other assemblers | |||
**Assembly analysis | |||
*Will formulate more detailed plan and discuss with Dr. Zhang |
Latest revision as of 20:34, 10 September 2013
Quick and Dirty Assembly Oncomelania Illumina contigs + moleculo data[edit]
Background[edit]
- Dr. Zhang previously performed soapdenovo assembly on a smaller Illumina dataset, found in </media/LTS_15T/Kun_LTS/Snail/HB_species/Snail.HB.Soap.trimmed.K27.scafSeq>
- We wanted to quickly check how incorporating moleculo data will help improve assembly, so we used celera assembler to do OLC assembly on contigs>100bp and all of the moleculo data (without filtering, using default settings)
- Test run is found in my genemapster: </media/disk-2/cjwei/130419_Oncomelania_Illumina_Moleculo/Illumina_contigs+Moleculo_Assembly>
Procedure[edit]
- Convert Illumina contigs to fastq file format using converter utility (will create artificial fastq by assigning quality score of I to each base) -> this is required for inputting file into Celera
- Go into folder <~/software/Hybrid_error_correction_assembly_software/wgs_download_2>
- Use command:
java convertFastaAndQualToFastq input_file > output_file
- Combined both Illumina contigs fastq file + Moleculo fastq file into new file: <Illumina_contig+Moleculo.fastq> (using cat command)
- It is necessary to have the correct ".fastq" file extension in order to continue forward
- Create .frg file for input to celera (this is the primary input for assembly that gives general data on the read file)
/media/2TB_store1/cjwei/software/Hybrid_error_correction_assembly_software/wgs_download_2/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname illumina_contigs_moleculo -reads Illumina_contig+Moleculo.fastq >Illumina_contig+Moleculo.frg
- Used "-reads" option because mimic single end reads for assembly
- RunCA to do assembly on combined dataset
~/software/Hybrid_error_correction_assembly_software/wgs-7.0/Linux-amd64/bin/runCA -d Illumina_contig+Moleculo_assembly -p Illumina_contig+Moleculo Illumina_contig+Moleculo.frg
- Without .spec file input, we are not doing correction as in normal hybrid assembly with pacbio+illumina data
Results[edit]
assembly | n | n:100 | n:N50 | min | median | mean | N50 | max | sum |
---|---|---|---|---|---|---|---|---|---|
Illumina contig + Moleculo | 10322 | 10322 | 2812 | 1000 | 2458 | 3094 | 3682 | 17558 | 31.94e6 |
Illumina contig | 2167043 | 2167043 | 785219 | 100 | 132 | 152 | 148 | 4661 | 329.4e6 |
- Results show a brief picture of the result of combining moleculo data with Illumina contigs. Overall, there is a dramatic increase in N50 and max contig length. However, there is a decrease in total bp assembled, probably because smaller contigs are being thrown out.
- Will need to run more detailed tests to better assemble the data. Brief future plan:
- Optimize assembly of Illumina reads using complete dataset
- Run SEQuel on the assembled contigs to improve assembly accuracy
- Hybrid assembly of Illumina contigs + Moleculo data -> will need to optimize assembly parameters for celera or explore other assemblers
- Assembly analysis
- Will formulate more detailed plan and discuss with Dr. Zhang