Analyses

FASTQC & MULTIQC

The rawdata obtained were quality checked by using the software FastQC. The commands used for this step can be seen in the code page. Thereafter, a scaffold was chosen to continue the other analyses with. The scaffold 10 was chosen and a script was done using the program multiqc (the script can be seen on the code page in section multiqc) so that the quality reports for scaffold 10 were gathered into a summary report instead. The generated summary reports from illumina, pacbio and the trancriptome were downloaded.

Illumina quality report

Pacbio quality report

Transcriptomic quality report

ej trimma på illumina, trimma de som är otrimmade . använd allt sen vid mapping. välj bara en scaffold.

CANU

The pacbio scaffold 10 data was assembled using the program canu. A script was made and can be seen in the code section and was runned with the command sbatch.

TRIMMOMATIC

The untrimmed transcriptomic data was trimmed using the program trimmomatic. A script was made and can be seen in the code section and was runned with the command sbatch.

BWA

Mapping of the illumina reads (scaffold 10 1P and scaffold 10 2P) and the assembled pacbio scaffold 10 data was done with the program BWA so that the assembly thereafter could be corrected with the illumina reads. The code can be seen in the code section and the script was runned with the command sbatch.

PILON

Improvement of the assembly was made by using the program pilon that required the assembly as imput as well as the aligned bam file from the previous step. A script was made and can be seen on the code page in the section pilon.

QUAST

Quality assessment was made with quast. The script can be seen on the code page in the section quast.