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Sequence Alignment Using Snap Tool

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.

sequence alignment bwa
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updated by anin.gregory anin.gregory • written by anju.cs15 • anju.cs15

3 answers

try MAUVE

• 235 views • link
written by Naren Naren

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

• 180 views • link
written by Istvan Albert Istvan Albert

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

• 0 views • link
written by anin.gregory anin.gregory

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