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Maggi-Chen / Inspector

A tool for evaluating long-read de novo assembly results
MIT License
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minimap2 -I option #10

Closed diego-rt closed 2 months ago

diego-rt commented 2 years ago

Hi,

Because of my genome size I need to specific the minimap2 -I parameter to a larger number. Is it possible to simply provide Inspector with the bam file rather than with a fastq file? It also would make things way easier when working on a cluster where I can distribute the mapping jobs.

Thanks!

Maggi-Chen commented 2 years ago

Hi,

Thank you for the suggestions. I think you can use your own sorted BAM with the '--skip_read_alignment' in Inspector. Basically you will need to:

  1. Align reads to assembly with minimap2 -I and sort BAM file
  2. Create a softlink to the sorted BAM file in the output directory of Inspector (make sure the BAM file is named as 'read_to_contig.bam')
  3. Run Inspector with --skip_read_alignment

This should work for your case. Pleas let me know if you have met ant problems with this.

Thanks.