Paired-end reads
simonepignotti opened this issue · 0 comments
simonepignotti commented
Add support for paired-end reads to the query
command.
Updated specification
Usage: prophex query [options] <index_prefix> <in1.fq> [in2.fq]
...
Behavior
Each pair should be concatenated and separated by a N
character.
The k-mers overlapping that position should have a specific marker in the output, e.g. C
(concatenation).
Example
k=4
in1.fq
:
@read1/1
ACGT
+
!!!!
...
in2.fq
:
@read1/2
TGCA
+
!!!!
...
Extended Kraken format
output:
U read1 0 8 ref1:1 C:4 ref1:1
Bitmask output format (#14 )
The hit and coverage masks should not contain the concatenation k-mers, but the two reads should be separated by a pipe (|
).
read1 ref1 8 2 8 1|1
Alternative solutions
If there is a cleaner way to obtain the same result without concatenating reads with N
, we should consider it (e.g. query the two parts indipendently).