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How to align paired-end Sanger sequences

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 !

alignment sequencing
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updated by trausch 202 • | written by jadeles 0

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.

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written by GenoMax 16K

Thank you for your answer !

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written by jadeles 0

1 answer

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
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written by trausch 202

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