Question: Ion Torrent Reference Assembly
1
gravatar for diltsjeri
6.8 years ago by
diltsjeri440
Chicago, IL
diltsjeri440 wrote:

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!

assembly ion-torrent reference • 3.8k views
ADD COMMENTlink modified 6.7 years ago by avik60 • written 6.8 years ago by diltsjeri440
3
gravatar for avik
6.8 years ago by
avik60
avik60 wrote:

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

ADD COMMENTlink written 6.8 years ago by avik60

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 REPLYlink written 6.8 years ago by diltsjeri440

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 REPLYlink written 6.8 years ago by Richard550
1
gravatar for Richard
6.8 years ago by
Richard550
Canada
Richard550 wrote:

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 COMMENTlink written 6.8 years ago by Richard550
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2250 users visited in the last hour