DAshow

DAshow

DAshow reads the database and local alignments file and displays it in a human readable format.

Example usage (for example, looking at the output of a FALCON workflow):

LAshow raw_reads.db job_0000/L1.1.6.las | less

The format of the output is:

<alignementfile>: <n> records
       a_read  b_read  flag [ a_start..a_end ] x [ b_start..b_end] : prec  n diffs  ( t trace pts)

where

a_read  : subread index from sequence a
b_read  : subread index from sequence b
flag    : 'c' (complemented) or 'n' (normal) alignment
a_start : base offset of the start of subread from sequence a
a_end   : base offset of the end of the subread from sequence a (inclusive)
b_start : base offset of the start of subread from sequence b
b_end   : base offset of the end of the subread from sequence b (inclusive)
prec    : '<' for non reference alignment and '=' for reference alignment
n       : number of differences between subreads within the alignment, counted in units of bases
t       : number of trace points inserted for these subreads

The brackets are shown as either square [] or angle <>  brackets. If the alignment runs to very start or end of 
the subread, the bracket is an angle bracket, otherwise the bracket is a square bracket.  For example, if the
a_start value is 0, then the bracket would be a '<' angle bracket. This is to alert the user that the alignment could
possibly have extended earlier in time if there had been sequencing data there, but it isn't there.

Example output:

$ LAshow raw_reads.db job_0000/L1.1.6.las  | head

L1.1.6: 720,350 records
       3   117,458 n   [ 7,587.. 8,656] x [ 4,128.. 5,209] :   <    141 diffs  ( 2 trace pts)
       3   117,732 c   [ 7,596.. 8,656] x [12,590..11,536] :   <    158 diffs  ( 2 trace pts)
       3   117,999 n   [ 7,587.. 8,656] x [12,425..13,508] :   <    141 diffs  ( 2 trace pts)
       3   119,283 n   [ 7,671.. 8,656] x [14,586..15,605] :   <    144 diffs  ( 2 trace pts)
       3   121,738 c   <     0.. 9,000] x [ 9,008..     0> :   <     77 diffs  ( 9 trace pts)
       3   122,068 n   [ 7,629.. 8,656] x [16,114..17,140] :   <    123 diffs  ( 2 trace pts)
       3   122,162 n   [ 7,596.. 8,664] x [ 5,812.. 6,882] :   <    124 diffs  ( 2 trace pts)
       3   126,304 n   [ 7,596.. 8,656] x [15,239..16,309] :   <    138 diffs  ( 2 trace pts)

The first line shows that subread 3 from the 'a' library overlaps with subread 117,458 from the 'b' library. The overlaps from the 'a' subread starts at base offset 7587 and goes to 8656, and from the 'b' subread starts at base 4128 and goes to 5209.