1. MapView: visualization of short reads alignment on a desktop computer
InCoB 2009
MapView: visualization of short reads alignment on a desktop computer
Hua Bao
Sun Yat-sen University

2. Next-generation sequencing
Sequencing by synthesis
High-throughput (tens of millions reads per lane)
Read length is short (25-50bp)
Sequencing error rate is relatively higher than Sanger sequencing

3. Statement of the problem
1. Alignment results: (e.g. , 50M reads)
read1 TATCGCACATAGTTCGCG hhhhhhhllhhhh;hA Chr
read2 CATACGACACTCATGTAG h,abhhhh;hAhhda, Chr2 94
2. Reference genome: (e.g. , 500M bp)
>Chr1
CGATCGAGCGACAGACGAGCACACGTAGCACTGTGGGGGAA
Visualization of large-scale alignment data with super-high computational efficiency.

4. Computational efficiency
Memory usage :
Data compressed
Fractional loading
CPU time :
Indexing
Pre-computing

5. File format design MapView format (MVF) : Head Data Index Statistics
Basic info of reference and reads
Offset of Data, Index and Statistics
Compressed sequences
Ordered alignments
The offset address of data is indexed by reference position
Coverage information of reference site
Head
Data
Index
Statistics

6. Loading algorithms MapView file Jump to different region MapView
window
MapView
window
Genomic position
Using Index
Offset address
Data
Data
MapView
file

7. Efficiency of MapView Computational efficiency comparision Tool
Version
Memory usage
CPU times
Consed
18.0
12.06 GB
208 s
Hawkeye
2.0.8
14.14 GB
296 s
EagleView
2.2
3.91 GB
207 s
MapView
3.1
0.04 GB
2 s
The alignment data for the assessment are of reference length
43 million bp and 6 million Illumina 44-bp reads.

8. User-friendly Interface

9. User-friendly Interface

10. User-friendly Interface

11. Summary Super-high computational efficiency：
Visualization of hundreds of millions reads with 40M memory in 2 seconds.
Rich featured and user-friendly:
Compact alignment view for both single-end and paired-end short reads, multiple navigation and zoom modes.

12. Thank you! MapView: visualization of short reads alignment
on a desktop computer
Thank you!