1. SOAP3-dp Workflow

2. Pair up the seed alignments
SOAP3-dp workflow for paired-end alignment
Step 1: Use SOAP3 to align pair-ended reads
paired alignments
Paired-end reads
chr 6, +4,059, -4,369;
………….
SOAP3 (2-mismatch)
…………………..
Step 2: For reads with one end mapped but another not, use Default-DP to align the unmapped ends
One ends’ alignments
Default-DP
chr 9, +49,538;
………..
…….….
paired alignments
mapped region
of one end
candidate region
for the unmapped end
chr 9, +49,538, -49,829;
…………. +
The unmapped ends
chr 9 +
49,538
……….
use DP to align
Step 3: For reads with both ends unaligned, use SOAP3 to align the seeds and then use Deep-DP to align both ends
seed alignments
of first end
seed alignments
of second end
SOAP3
(1-mismatch)
chr 18, +349,683;
…………. +
chr 18, -349,998;
………….
seeds
Pair up the seed alignments
Deep-DP
paired alignments
candidate region
chr 18
paired seed alignments
chr 18, +349,664, -349,923;
………….
349,683 +
349,998 -
chr 18, +349,683, -349,998;
………….
use DP to align

3. Step 1: SOAP3 Both ends can be mapped and paired properly
Report the alignments
Only one end can be mapped
with not too many hits (i.e. <= 30)
Store the readID (of aligned end) and hits to ARRAY A
SOAP3 (2-mismatch)
Only one end can be mapped
with too many hits (i.e. > 30)
A read pair is paired properly if:
Both ends are mapped within the insert size (i.e. a range of distance between two ends inputted by the user).
In proper orientation (for illumina reads, the end aligned to left side is in forward strand, while another aligned to right in reverse strand.)
Store the readID ( of aligned end) and hits to ARRAY B
both ends cannot be mapped
Store the readID (of the first read of the pairs) and hits to ARRAY C
Both ends can be mapped but not paired properly
Store the readID and hits to ARRAY A or B
(describe more in next slides)

4. Step 1: SOAP3 -- Both ends can be mapped but not paired properly
read 1
read 2
Not paired properly
YES
YES
Let x = # of all valid hits of read 1
Let y = # of all valid hits of read 2
If x > 30, only retains the best hits of read 1 and reset x = # of best hits of read 1.
If y > 30, only retains the best hits of read 2 and reset y = # of best hits of read 2.
a) x,y <= 30
YES NO NO
YES
ARRAY A
b) x <= 30 < y
YES NO
ARRAY A
c) y <= 30 < x NO
YES
ARRAY A
d) 30 < x < y
YES NO
ARRAY B
e) 30 < y <= x NO
YES
ARRAY B
Store the read ID and hits of YES to ARRAY A or B

5. default DP and new default DP
Step 2 and step 3:
default DP and new default DP
Both ends can be mapped and paired properly
Report the alignments
Otherwise
Default DP
Array A
Store the readID of the first read of the pairs to ARRAY C
Both ends can be mapped and paired properly
Report the alignments
Otherwise
New default DP
Array B
Store the readID of the first read of the pairs to ARRAY C

6. Detailed picture of Default DP and New Default DP
For reads with one end mapped but another not, AND the number of hits is not too many,
use Default-DP to align the unmapped ends
One ends’ alignments
Default-DP
chr 9, ;
………..
…….….
paired alignments
mapped region
of one end
candidate region
for the unmapped end
chr 9, , ;
…………. +
The unmapped ends
chr 9 +
49538
……….
use DP to align
For reads with one end mapped but another not, AND the number of hits is too many,
use New-Default-DP to align the unmapped ends
seed alignments
of unmapped end
One ends’ alignments
The unmapped ends
SOAP3
(1-mismatch)
chr 18, ;
………….
chr 18, ;
………..
…….….
seeds +
seeds
Pair up the seed alignments
with the alignments of another end
New-Default-DP
paired alignments
candidate region
chr 18
chr 18, , ;
………….
349683 +
349998 -
chr 18, , ;
………….
mapped region
of one end
use DP to align

7. Step 4: 2-level Deep DP ARRAY C ROUND 1 SEEDING for both ends
Seed length: 26
Sample rate: 1/13
Max # of hits allowed: 100
If (1) there exists a seed with
too many hits; AND
(2) no pairs of hits
within insert size.
If there exists pairs of
hits within insert size.
If there exists pairs of
hits within insert size.
Perform DP
for those pairs of hits within insert size.
ROUND 2 SEEDING for both ends
Seed length: 30
Sample rate: 1/15
Max # of hits allowed: 1000
Case 1: Valid paired alignments found
Report the alignments
Case 2: No valid paired alignment found
Store the readID of both ends to ARRAY D

8. Report the ends cannot be aligned
Step 5:
Single DP
The end can be mapped
Report the alignments
Otherwise
Single DP
Array D
Report the ends cannot be aligned

9. Detailed picture of Single DP
seed alignments
SOAP3
(1-mismatch)
chr 18, +349,683;
………….
seeds
Single-DP
Report the alignments
Candidate region
Chr18
chr 18, +349,664;
………….
349,683 +
use DP to align

10. Paired-end alignment (overall workflow) Load 6M reads (3M pairs)
SOAP3 (2-mismatch)
Create a new CPU thread
to load next 6M reads
New default DP
Note: New-default DP needs 2BWT in GPU, while default DP does not. Thus we run new-default DP before default DP,
because after SOAP3, 2BWT index is already inside GPU.
Default DP
2-level deep DP
single DP
Yes
More reads to process? No
END

11. SOAP3 Architecture …….. …….. Host (CPU) Device (GPU) 2BWT + SA 2BWT
Execution
Host (CPU)
Execution
Device (GPU)
Memory-resident data structures
Memory-resident data structures
2BWT + SA
2BWT
Process 1M reads for round 1 and round 2 alignments
Process 1M reads for round 1 and round 2 alignments
Process round 3 alignment &
Report results
Process round 3 alignment &
report results
Process 1M reads for round 1 and round 2 alignments
Mention hard reads may be processed in multiple GPU rounds
Mention there are many cases
Process round 3 alignment &
report results
Process 1M reads for round 1 and round 2 alignments
Process round 3 alignment &
report results
Process 1M reads for round 1 and round 2 alignments
……..
……..

12. DP with seeding …….. …….. Host (CPU) Device (GPU) 2BWT + SA
Execution
Host (CPU)
Execution
Device (GPU)
Memory-resident data structures
Memory-resident data structures
2BWT + SA
2BWT / DP tables
Copy 2BWT index to GPU &
Extract seeds of reads in Array C
SOAP3
(1-mismatch)
Process 1M seeds for round 1 and round 2 alignments
Process 1M seeds for round 1 and round 2 alignments
Process round 3 alignment
Mention hard reads may be processed in multiple GPU rounds
Mention there are many cases
……..
……..
Pair-up the seed alignments,
Clear 2BWT index in GPU & Create DP tables in GPU
Perform DP between the reads and the candidate regions

13. Perform DP between the reads and the candidate regions
Default DP
Execution
Host (CPU)
Execution
Device (GPU)
Memory-resident data structures
Memory-resident data structures
2BWT + SA
DP tables
Create DP tables in GPU
Perform DP between the reads and the candidate regions
Mention hard reads may be processed in multiple GPU rounds
Mention there are many cases

14. Load 6M single-end reads
Single-end alignment
(overall workflow)
Load 6M single-end reads
SOAP3 (2-mismatch)
Create a new CPU thread
to load next 6M reads
single DP
Yes
More reads to process? No
END

15. Paired-end alignment (For read length > 150)
Load 6M reads (3M pairs)
2-level deep DP
Create a new CPU thread
to load next 6M reads
single DP
Yes
More reads to process? No
END