Key Parameters Used within FlexTyper

Sliding Search Parameters

"Parameters for Sliding Searches"

Centered Search Parameters

"Parameters for Centered Searches"

Non Unique Kmers

If two query sequences contain an identical kmer, then that kmer is flagged as a ‘non unique kmer’.

Over Counted Kmers

If a kmer search returns too many positions, then that kmer is disregarded as uninformative and flagged as an “over counted kmer”.

Count As Pairs

For paired reads [R1 = <1,1>, R2 = <1,2>]

If countAsPairs = true, then if a query matches R1 and R2, then the query count is only one.

Unique Reads

For two queries Q1 and Q2, uniqueReads = true, then if a read, R, matches Q1 and Q2, then R will be removed from the set of matching read hits for both Q1 and Q2.

Combining countAsPairs and uniqueReads

Suppose you have 3 sets of paired reads:

Pair 1: [R1 = <1,1>, R2 = <1,2>]

Pair 2: [R3 = <2,1>, R4 = <2,2>]

Pair 3: [R5 = <3,1>, R6 = <3,2>]

And two query sequences with matching read hits:

Query 1 = [R1, R3, R5, R6]

Query 2 = [R1, R4]

Expected Results

	countAsPairs=True			countAsPairs= False
	Query	Read Hits	Count	Query	Read Hits	Count
uniqueReads = True	1	[R5, R6]	1	1	[R3,R5,R6]	3
	2	[ ]	0	2	[R4]	1
uniqueReads = True	1	[R1, R3, R5, R6]	3	1	[R1,R3,R5,R6]	4
	2	[R1, R4]	2	2	[R1,R4]	2