Recommended aligner to use with a draft reference genome and paired end reads

[N311V]

Hi All,

Just wondering if anyone can suggest which aligner to use with a draft reference genome (read 5799 scaffolds ranging from 95 to 6,200,209bp with an N50 of ~1.2Mbp) and Illumina 100bp paired end data.

Would you expect a particular aligner to work better (faster and/or more accurate) than others.

Thanks

[shi]

Hi @N311V,

You may try the Subread aligner. Have a look at this post for more information.

http://seqanswers.com/forums/showpost.php?p=100879&postcount=1

Cheers,
Wei

[jimmybee]

Depends on your sequencing and the characteristics of your reference sequence. I don't think having a draft (rather than 'more' finished) sequence does a lot for the accuracy of the alignment tbh.

Every aligner has advantages and disadvantages so the best way to know is to try them all