Genome draft sequences

Question

[alzahare1985]

Hi dears,

I want to align bacterial genome draft to its paired - end reads .. Which tool? how to do it ?

one more question , what is the guideline for genome draft validation ?

Best Regards Maytham Abbas Alzuhairi

[h.mon]

I want to align bacterial genome draft to its paired - end reads

You should map the reads to the draft genome, not the opposite. You can use BWA or Bowtie2 for this task.

For assembly evaluation, good tools are BUSCO and QUAST. BlobTools may be interesting to check for contamination.

edit: my original answer bellow does not address exactly your question.

See Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data and Update to Comparative Bacterial Genomics tutorial.