How to Check the Quality of a .fasta File for Sequence Alignment?

Question

[Dikshya]

I have a .fasta file, and I need to check its quality for sequence alignment. Is there a method to assess the quality of a .fasta file?

[Pierre Lindenbaum]

a fasta file is a text file containing the names and the sequences of DNA/protein entities. What is the quality of such file ?

[1769mkc]

you mean fastq?

[colindaven]

Do you mean a genome fasta ? In that case you can use tools like Inspector https://github.com/Maggi-Chen/Inspector or Flagger on github to check the assembly prior to alignment. If you have FASTQ, not FASTA, then use the tool FASTQC.

Answer 1

[GenoMax]

There is no way to check "quality" of a plain fasta file, since there are no confidence scores associated with the sequence. Aligning the fasta to the reference of choice may actually provide an indication of quality based on the alignment. Especially if you expect the sequence to align end-to-end with few/no SNP/indels etc.