Sequence Alignment Using Snap Tool

Question

[anju.cs15]

can anyone tell me about performance of SNAP sequence aligner tool, and its comparision with other existing tools like novoalignmpi, BWA and Bowtie, in terms of speed on multi-core system and accuracy. Actually i have tested SNAP on 48-core machine, and it does alignment in 22 minutes , with read file size 1.8GB & 1.8 GB. I want a confirmation that is it faster than novoalignMPI. I am from computer science background, so i dont have much idea about others tool.

thank you.

Answer 1

[Naren]

try MAUVE

Answer 2

[Istvan Albert]

There is a lot to performance than just runtime. Moreover the genome structure and how well the reads align may also greatly impact this performance. Here is a page that demonstrates a better way to compare alignment tools;

http://lh3lh3.users.sourceforge.net/alnROC.shtml

Answer 3

[anin.gregory]

try Mugsy (http://mugsy.sourceforge.net/)