bwa MEM for illumina 1.3+
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7.2 years ago

I see that BWA ALN has an "-I" flag for changing the quality of the reads.  I don't see this option for BWA MEM? Does anyone know if I'm missing something?

mapping bwa phred quality • 2.7k views
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You're not missing anything: Bwa Mem: How To Specify The Fastq Phred Format? (see my link to a bwa email list message about this from Heng Li).

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what is the size of your reads ? See Heng's comment:Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem

BWA-MEM however lacks the following features:

  • Working with very short reads. The performance and the accuracy of BWA-MEM will degrade.
  • Guaranteed sensitivity to hits within a certain edit distance threshold (as with BWA and GEM).
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100bp.  I wanted to use mem for consistency across some simulations and real data.

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Honestly, I was stuck between mem and aln for my 100bp data, and aln performed much better, more reads aligned.

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7.0 years ago

You can use my reformat tool to change ASCII-64 qualities to ASCII-33 (and most other format conversions).  It supports piping from stdin and to stdout, so you don't have to write a temp file.  And it's the fastest format convert of which I am aware.

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