aligner for CORRECTED pacbio long reads

Question

[cmo]

After error-correcting PacBio long reads using Illumina short-reads, what aligners are adept for aligning the corrected PacBio long reads against the genome?

Should I think of the corrected PacBio reads as just "long Illumina reads" (in terms of error & indel rate, etc.) ?

I am tempted to use BLASR, but the PacBio-specific error rates and indels are presumably "corrected out", so it still appropriate to use BLASR?

Is it appropriate to use BWA for the corrected PacBio long-reads?

Are some aligners more appropriate than others?

[jrsmith]

CMO, your best bet for working with hybrid data (short read + long read) is to use a hybrid aware package like one of the two options below:

• ECTools
• MHAP - PBcR

The details of how hybrid data is correctly combined and then processed downstream is more complicated than most would expect. The long-and-short (pun intended) of it is that any tools written to process long-read data alone (BLASR) or short-read data alone( BWA etc.) are non-optimal.

[cmo]

Thank you, but I am more interested in how to align after the PacBio long reads are corrected. I am not necessarily interested in a de-novo assembly. And the correction step should be taken as given, I am not interested in correction methods.

[buchananbuck01]

Hi CMO,

I'm not a SME on the RS II so I ask Jason and he was kind enough to respond -- hope it was helpful...

Answer 1

[rhall]

I would suggest using Blasr, even with default parameters the alignment of corrected reads should be high quality, and parameters could be altered to more optimally map low error long reads, although I'm not sure you would gain anything other than performance (speed). Another option would be blast, while bwa would probably work you are more likely to run into issues with performance and read length, particularly if your corrected reads are at the top end >40kb.

[lh3]

Bwa-mem works for this type of data.

Answer 2

[orange]

pacbio suggest that use blasr or bwa. https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Evaluating-Assemblies

[Lalit]

The link is not working.

[gconcepcion]

This is a very old and outdated link, what is it exactly that you are trying to do?

Align PacBio HiFi reads to a reference?

Try minimap2: https://github.com/lh3/minimap2

[Lalit]

Thanks, I will use minimap2

Answer 3

[Felix Francis]

I would use bwa mem or BLASTn rather than blasr for better specificity. I have had experience with mapping error corrected PacBio reads using blasr and some of the best hits were incorrect.