qseq and sseq in -outfmt 6 are not aligned


New member

I recently realised that in the output format '-outfmt 6' the 2 fields 'qseq' and 'sseq' do not correspond to the aligned sequences, but rather to the sequences that align (i.e. the string of characters (aa or nucl) without the insertions and deletions).
That is different to the corresponding 'qseq' and 'sseq' output in BLAST, in which indels are present.

nb: however, it seems that insertions and deletions (indicated by series of '---') are present in the XML output format (fields Hsp_qseq and Hsp_hseq).

I was wondering if it would be possible to 'put back' the indels in the tabular output format (-outfmt 6), for the seek of compatibility with BLAST format.

many thanks

Benjamin Buchfink

Staff member
Hi Romain,

no problem, I will add that feature, but probably make it a new output field instead of changing the behaviour of the current ones, otherwise it will break the compatibility with previous Diamond versions.

Best regards,