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How do concatenate different fasta file
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16 months ago
lkianmehr • 30
France

Does anybody know what is the best and trustable way to concatenate different FASTA files for making them index together?

thanks in advance

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7 weeks ago
genomax 68k
United States

Just cat them together. I am not sure what you mean by trustable?

If you have spaces in the headers (e.g. words separated by names) make sure to change the space to _. Most aligners will drop things past first space when reporting alignments (e.g. bbmap is an exception and will keep the entire name by default unless you use trd=t). You may get confusing results if the part of name up to first space is common to more than one record.

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14 months ago
Belgium, Brussels

As Genomax commented :

In a unix shell :

cat file1.fasa file2.fastq file3.fasta > merged_file.fasta

or even easier if all your fasta files are in a directory and ends by .fasta

cat *.fasta > merged_file.fasta
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I tend to remember that there were cases (also reported here on Biostars) when cat *.fasta somehow caused an infinity loop because the output file would be constantly appended to itself (as it also ends on .fasta). To avoid this, consider to use:

find . -maxdepth 1 -name \*.fasta | xargs cat > output.fasta
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that's a good point !

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