Hi everyone,

In order to polish my Falcon assembly of my D. suzukii genome, from PacBio long reads, I need to align the raw reads to my genome and create a .bam or a .sam file.

Such a tool already exist at PacBio, called blasr, but is currently not working (the 5.3 version I've installed do not provide a .bam or a .sam output... Which is VERY annoying).

Does an alternative of such aligner exist ? It has to be a aligner aware of the higher error rate of PacBio reads (that's why I can't use a classic aligner).

Any ideas ? I'm truely desesperate, I absolutely need to polish my assembly before going further in my analysis.

Thanks for your help !

Roxane
bwa and BBmap (as far as I know limited to 6kb)
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>PacBio subreads or Oxford Nanopore reads to a reference genome:  
``` bwa mem -x pacbio ref.fa reads.fq > aln.sam ```

more [here](http://www.homolog.us/blogs/blog/2013/10/23/bwa-mem-blasr-look-pacbios-newly-released-human-data/)

**Update**. 

[Minimap2][1]

>  is a versatile sequence alignment program that aligns DNA or mRNA
> sequences against a large reference database. minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, [NGMLR][2] and GMAP.


  [1]: https://github.com/lh3/minimap2
  [2]: https://github.com/philres/ngmlr