How to align paired-end Sanger sequences

Question

[jadeles]

Hi all,

I would like to align and create a consensus sequence from paired end Sanger sequences. Each pair is named as follows : >XX_F and >XX_R. Each pair should align on a few to hundreds of nucleotides. Do you know any software/codes I could use to do that ?

Thank you !

[GenoMax]

You can use merger program from EMBOSS package to merge the individual reads. Here is a web-front end for that tool, if you prefer using that.

[jadeles]

Thank you for your answer !

Answer 1

[trausch]

You can use tracy to patch a reference using Sanger sequences. It's a reference-guided algorithm to assemble Sanger traces and it also creates a consensus sequence.

tracy assemble -r reference_slice.fa forward.ab1 reverse.ab1