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I have several .ab1 files generated from Chromas. I want to merge all of them into a single FASTA sequence file. How can I do this in an automated way?

Note that I don't have Chromas installed (the files were generated by someone else). I am using linux, so open-source, command line tools are preferred.

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In general you should use a base calling algorithm to generate the sequences from the chromatogram and not directly convert it to fasta (Courtesy: Sven [SEQanswers] ). As mentioned in the link, phred and TraceTuner are popular base calling software that can generate a fasta output.

The software mentioned by The Nightman can be used for converting .ab1 to fasta. You can also try this BioPython module called abifpy. You can easily read each .ab1 file, using a python script, and write the sequences in fasta format as a single file.

Combining multiple fasta is quite trivial. You can use cat as mentioned by others.

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DNA Baser has a batch abi to fasta converter here. After files have been converted to .fa files, they can be concatenated together in UNIX/MAC using cat *fa > output.fa

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Typical possibilities that come to mind are programs available in EMBOSS and Staden. However the question of how to access the sequence data stored in .ab1 files has been asked on Biostars a number of times, so I suggest having a look at the various answers there for options that are suitable for your environment and use case, see Biostars search "ab1".

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