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JiaoLaboratory / CRAQ

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
https://doi.org/10.1038/s41467-023-42336-w
MIT License
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Can I use ont and HiFi data at the same time? #7

Closed Bank-tidy closed 7 months ago

Bank-tidy commented 7 months ago

Hello, Thank you for developing a very useful tool,I have some doubts about using the tool, so I woulld like to ask you for advice:

$ craq -g assembly.fa -sms SMS.fa.gz -ngs NGS_R1.fa.gz,NGS_R2.fa.gz -x map-hifi Can I input both of ONT and hifi data at the same time in this step: -ngs ?

$ craq -g assembly.fa -sms SMS_sort.bam -ngs NGS_sort.bam Or input both of the BAM files of ONT and hifi data at the same time in this step: -ngs ?

JiaoLaboratory commented 7 months ago

Sorry, CRAQ cannot take input simultaneously from ONT and HIFI data (.fastq format). Because existing different between ONT and HiFi data. However, you can merge the BAM files of the two datasets using samtools with the command 'samtools merge SMS_merge.bam HIFI.sort.bam ONT.sort.bam' and then use the merged 'SMS_merge.bam' as input. Additionally, the '-ngs' option requires short-reads as input; if you only have HIFI and ONT data, simply execute 'craq -g assembly.fa -sms SMS_merge.bam' is ok."

Bank-tidy commented 7 months ago

Thank you for your suggestion！