Tools/software for assembling .ab1 trace files

Question

[nomorewords]

Hello Fellow Bioinformaticians,

I'm trying to find a tool to assemble .ab1 trace files (ABI sequencer data files), ideally in Python. However, it looks like Biopython doesn't support DNA assembly. I was wondering if you have any recommendations or suggestions?

Thank you very much!

[vytarasov]

If you have Mac you can use BioLabDonkey program to assemble the reads from .ab1 files directly.

About assembly of .ab1 reads in BioLabDonkey

Answer 1

[Michael]

A more recent solution is Tracy. An open-source trace file toolkit.

[nomorewords]

I went with calling Tracy from python scripts, thank you!

Answer 2

[Mensur Dlakic]

I'd be surprised if such a tool existed that assembles directly from ab1 files. You may be able to convert .ab1 files into .fastq format as described here. Then you can assemble the converted reads using MIRA, SPAdes, phrap or some other assembler that can use Sanger reads. You may also want to check out phred which is part of the phrap suite, as it also can read and convert .ab1 files.

[Michael]

Indeed, phred/phrap/consed is the standard toolkit for Sanger assembly. One can still get them, but they existed before python was even a thing.

Answer 3

[sklages]

Depending on the size of the sanger dataset and if you are fine with commercial software, you might want to consider packages like Genious.

Working with MIRA or even phrap is fun but probably very time-consuming nowadays, especially if you are not familiar with assembly file formats. Staden Package or Consed may be used as alignment editors.

I have been working with these packages years ago ..