text: user16067: I just ran an assembly on yeast genomes using Flye and I want to polish those assemblies with Pilon but it requires a sorted BAM file.
  How do I make a BAM file of the resulting assembled.fasta?
  
  user37: Run a short-read mapper. For example:
  bwa index assembled.fasta
  bwa mem -pt16 assembled.fasta read1.fq.gz read2.fq.gz \
    | samtools sort -m4G -@4 -o align.bam -
  
  
original_text: 16067: <p>I just ran an assembly on yeast genomes using Flye and I want to polish those assemblies with Pilon but it requires a sorted BAM file.</p>
  <p>How do I make a BAM file of the resulting assembled.fasta?</p>
   37: <p>Run a short-read mapper. For example:</p>
  <pre><code>bwa index assembled.fasta
  bwa mem -pt16 assembled.fasta read1.fq.gz read2.fq.gz \
    | samtools sort -m4G -@4 -o align.bam -
  </code></pre>
  