<p>Hi,</p>

<p>I've been using the blastn (version 2.2.28+) standalone tool against a custom formatted genome via:</p>

<pre><code>blastn -db BLASTDB -word_size 7 -query input.fa -out filename -perc_identity 100 -outfmt 6 -max_target_seqs 2
</code></pre>

<p>To discard non-perfect hits and show only the 2 top hits.</p>

<p>The output file has a great format however is there a way to add an extra column that contains the actual target-seq (sequence of the matched hit)? Such that the fields are:</p>

<pre><code>query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, sequence
</code></pre>

<p>Thanks!</p>

<ul>
<li>TJC</li>
</ul>

Run `blastn -help` then look for the field called `outfmt`

    *** Formatting options
     -outfmt <String>
       alignment view options:
         0 = pairwise,
         1 = query-anchored showing identities,
         2 = query-anchored no identities,
         3 = flat query-anchored, show identities,
         4 = flat query-anchored, no identities,
         5 = XML Blast output,
         6 = tabular,
         7 = tabular with comment lines,
         8 = Text ASN.1,
         9 = Binary ASN.1,
        10 = Comma-separated values,
        11 = BLAST archive format (ASN.1) 
    
       Options 6, 7, and 10 can be additionally configured to produce
       a custom format specified by space delimited format specifiers.
       The supported format specifiers are:
               qseqid means Query Seq-id
                  qgi means Query GI
                 qacc means Query accesion
              qaccver means Query accesion.version
                 qlen means Query sequence length
               sseqid means Subject Seq-id
            sallseqid means All subject Seq-id(s), separated by a ';'
                  sgi means Subject GI
               sallgi means All subject GIs
                 sacc means Subject accession
              saccver means Subject accession.version
              sallacc means All subject accessions
                 slen means Subject sequence length
               qstart means Start of alignment in query
                 qend means End of alignment in query
               sstart means Start of alignment in subject
                 send means End of alignment in subject
                 qseq means Aligned part of query sequence
                 sseq means Aligned part of subject sequence
               evalue means Expect value
             bitscore means Bit score
                score means Raw score
               length means Alignment length
               pident means Percentage of identical matches
               nident means Number of identical matches
             mismatch means Number of mismatches
             positive means Number of positive-scoring matches
              gapopen means Number of gap openings
                 gaps means Total number of gaps
                 ppos means Percentage of positive-scoring matches
               frames means Query and subject frames separated by a '/'
               qframe means Query frame
               sframe means Subject frame
                 btop means Blast traceback operations (BTOP)
              staxids means Subject Taxonomy ID(s), separated by a ';'
            sscinames means Subject Scientific Name(s), separated by a ';'
            scomnames means Subject Common Name(s), separated by a ';'
           sblastnames means Subject Blast Name(s), separated by a ';'
                    (in alphabetical order)
           sskingdoms means Subject Super Kingdom(s), separated by a ';'
                    (in alphabetical order) 
               stitle means Subject Title
           salltitles means All Subject Title(s), separated by a '&lt;&gt;'
              sstrand means Subject Strand
                qcovs means Query Coverage Per Subject
              qcovhsp means Query Coverage Per HSP