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 : read index from sequence a
b_read : read index from sequence b
flag : 'c' (reverse-complemented) or 'n' (normal) alignment. If 'c' is shown, then
the start/end indices of the 'b' alignment will be reversed to make it clear
that it is the opposite orientation of the 'a' alignment..
a_start : base offset of the start of read from sequence a
a_end : base offset of the end of the read from sequence a (inclusive)
b_start : base offset of the start of read from sequence b
b_end : base offset of the end of the read from sequence b (inclusive)
prec : '<' for non reference alignment and '=' for reference alignment
n : number of differences between reads within the alignment, counted in units of bases
t : number of trace points inserted for these reads
The brackets are shown as either square [] or angle <> brackets. If the alignment runs to very start or end of
the read, 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 read 3 from the 'a' library overlaps with read 117,458 from the 'b' library. The overlaps from the 'a' read starts at base offset 7587 and goes to 8656, and from the 'b' read starts at base 4128 and goes to 5209. The single '<' after the colon ':' means this is not an alignment to a reference, so the number of diffs is an upper limit on real diffs. The number of differing bases appears follow by the number of trace points that were used to describe the alignment.
The second line shows a reverse-complemented alignment, by showing 'c' in the 3rd column and also reversing the indices of the 'b' alignment (i.e. 12590 comes first followed by 11536).
The fifth line shows an alignment where the alignment started at the start of the read, so instead of a square bracket '[', an angle bracket '<' is used.