Review default Blast output format

[laughedelic]

Here is the current default:

• qseqid
• qlen
• qstart
• qend
• sseqid
• slen
• sstart
• send
• bitscore
• sgi

---

Changes:

• sgi column should be removed

[eparejatobes]

Yes, sgi should be removed

[eparejatobes]

needs ohnosequences/blast-api#27

[eparejatobes]

need to update to ohnosequences/blast-api 0.5.0

[laughedelic]

What else has to be changed regarding default Blast output format? Add evalue column?

[rtobes]

This is probably related with your question: https://github.com/ohnosequences/pacbio16s/issues/3#issuecomment-198767138

[eparejatobes]

case object defaultBlastOutputRecord extends BlastOutputRecord(
  // query
  qseqid      :×:
  qstart      :×:
  qend        :×:
  qlen        :×:
  // reference
  sseqid      :×:
  sstart      :×:
  send        :×:
  slen        :×:
  // alignment
  evalue      :×:
  score       :×:
  bitscore    :×:  
  length      :×:
  pident      :×:  
  mismatch    :×:    
  gaps        :×:  
  gapopen     :×:  
  qcovs       :×:
  |[AnyBlastOutputField]
)

[rtobes]

What is qcovs, coverage of the alignment over the length of the query?

[eparejatobes]

@rtobes is hard to find a precise definition. This is the best I got:

• https://www.biostars.org/p/121972/#122201

[rtobes]

Thanks!

It is the percent of no. of bases in the query sequence aligned with the subject sequence (match or mismatch). The bases can be in one HSP or several HSPs (overlap) but they are counted only once. Gaps (in the subject sequence) are treated as mismatches.

If this final sentence is true qcovs is a really good parameter

[eparejatobes]

yup, that's why it's there in defaults :+1:

[laughedelic]

Done.