<p>Hi all,</p>

<p>I'm about to align a set of short reads on the genome after an <strong>exome</strong> capture.</p>

<p>I wonder if it would be worth to <strong>replace all the non-genic genomic sequences with 'N'.</strong></p>

<p>Wouldn't it speed up the alignment with BWA ? What would be the other possible consequences ? Has it ever been done before ?</p>

<p>Many thanks</p>

<p>Pierre</p>

<p>In a word, no. It's not necessary for any of the BWT aligners. In fact it would cause you to miss any unannotated exons, or possibly entire novel genes. It would also hide other biological events, such as genomic sequence contamination in the preparation process.</p>
<p>If you want to speed up the alignment, split the reads into several chunks and map them in parallel. Afterwards use a merging program such as samtools or Picard to create a single BAM file. We usually aim for ~ 1Gbp per process for a vertebrate genome.</p>