Question

Ion Torrent Reference Assembly

1

Entering edit mode

12.5 years ago

diltsjeri ▴ 470

What is the best reference assembler to use with ion torrent data? I can only seem to find information on Ion Torrent de novo assemblies, which is not what I'm looking for. Thanks in advance!

ion-torrent reference assembly • 5.8k views

ADD COMMENT • link updated 12.4 years ago by avik ▴ 60 • written 12.5 years ago by diltsjeri ▴ 470

score 3 · Answer 1 · 2012-05-15

3

Entering edit mode

12.5 years ago

avik ▴ 60

For ref mapping you may try TMAP https://github.com/iontorrent/TMAP

ADD COMMENT • link 12.5 years ago by avik ▴ 60

0

Entering edit mode

Could you clear something up for me? Is TMAP okay to use for reference assemblies, because reference assemblies use alignment techniques? (unlike de novo).

ADD REPLY • link 12.5 years ago by diltsjeri ▴ 470

0

Entering edit mode

TMAP will just do the alignment. However, if you are looking for an assemly there may be a package that will run on a bam file (created by TMAP) that will do that for you. If not there should be one :)

ADD REPLY • link 12.5 years ago by Richard ▴ 590

score 1 · Answer 2 · 2012-05-15

1

Entering edit mode

12.5 years ago

Richard ▴ 590

I've heard of people having decent success with MIRA, although I haven't tried it myself http://www.chevreux.org/projects_mira.html

ADD COMMENT • link 12.5 years ago by Richard ▴ 590