Pacbio: How to generate Unitigs.fa for ECTools correst.sh ?

Question

[GouthamAtla]

Hi,

I am trying to run ECTools's correct.sh script on PacBio reads. This shell script requires a unitigs file.

https://github.com/jgurtowski/ectools/blob/master/correct.sh

#path to high identity unitigs.

I would like to know how to generate the unitigs.fa file. If any one has experience analysing pacBio data, help me.

Answer 1

[richard.james.hall]

The unitigs fie contains the short read assembly that is to be used to correct the PacBio long reads, This could be generated via Celera Assembler:

http://wgs-assembler.sourceforge.net/wiki/index.php/Yersinia_pestis_KIM_D27,_using_Illumina_paired-end_reads,_with_CA8.1

Or a de bruijn graph assembler such as Abyss.

[GouthamAtla]

Thank you. I have also contacted pacbio support. Its the short read assembled data.