Question: Quality check of sequences in fasta format
0
gravatar for Fid_o
7 months ago by
Fid_o20
Fid_o20 wrote:

Hello,

I have .FASTA files of bacterial genomes. I want to check quality of the sequences. Which program accepts quality analysis of .FASTA files?

Cheers!

alignment assembly genome • 357 views
ADD COMMENTlink modified 7 months ago by genomax92k • written 7 months ago by Fid_o20

What kind of quality are you referring to?

If it means how "complete" is the genome then there are tools like BUSCO for that purpose.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax92k

@genomax, I mean to check the quality like we would check using FASTQC. I realise FASTQC takes in Fastq files, I have .FASTA files.

ADD REPLYlink written 7 months ago by Fid_o20

You can't. Fasta format does not allow for encoding of quality scores.

Note: There is an [fasta/qual format] which basically splits a fastq files into sequence/quality files (used by 454 I think). I don't think that is very prevalent. Do you have files like that by any chance?

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax92k

@genomax I don't have the fasta/qual files, it's just the fasta files.

This being the case, can I safely convert fasta files to fastq for purpose of FASTQC use? My first reservations with conversion would be possibility of introducing errors to the files.

ADD REPLYlink written 7 months ago by Fid_o20
1

can I safely convert fasta files to fastq for purpose of FASTQC use?

While you can do that it is meaningless in terms of analysis. You would set an artificial Q scores for each base. BTW, why do you need quality scores for your fasta files?

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax92k

@genomax. Thank you for your replies. I needed quality check for my SNP analysis on these sequences.

ADD REPLYlink written 7 months ago by Fid_o20
1

Not much you can do if you just have fasta sequence. Look for multiple reads (bases) supporting a particular call.

ADD REPLYlink written 7 months ago by genomax92k

Thank you for that help and insight. Absolutely helpful.

ADD REPLYlink written 7 months ago by Fid_o20
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