Question

Sequence Alignment Using Snap Tool

1

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11.0 years ago

anju.cs15 ▴ 20

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 • 3.8k views

ADD COMMENT • link updated 11.0 years ago by anin.gregory ▴ 110 • written 11.0 years ago by anju.cs15 ▴ 20

score 3 · Answer 1 · 2013-05-09

3

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11.0 years ago

Naren ▴ 1000

try MAUVE

ADD COMMENT • link 11.0 years ago by Naren ▴ 1000

score 2 · Answer 2 · 2013-05-09

2

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11.0 years ago

Istvan Albert 100k

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

ADD COMMENT • link 11.0 years ago by Istvan Albert 100k

score 0 · Answer 3 · 2013-05-14

0

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11.0 years ago

anin.gregory ▴ 110

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

ADD COMMENT • link 11.0 years ago by anin.gregory ▴ 110