Analyses

FASTQC

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 the quality reports for that scaffold 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 and the assembled pacbio scaffold 10 data was done 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.