Question: reuse of compiled reference genome indices (BWA, Bowtie, Hisat etc)
gravatar for marongiu.luigi
9 months ago by
Germany, Mannheim, UMM
marongiu.luigi340 wrote:


I understand that is always better to compile the reference genome indices on a given machine for the different aligners such as BWA, Bowtie2 and HiSat. However, the human genome takes a long time to be processed.

In order to avoid loosing so much computational power, is it possible to re-use (that is, copying them from one machine to another) the indices on machines with the same architecture, let's say AMD processors or Linux 64 bit environment?

What are the restrains one should look at when re-using the indices? otherwise one could simply use the pre-compiled indices available online.

Thank you

next-gen assembly genome • 274 views
ADD COMMENTlink modified 9 months ago by Devon Ryan86k • written 9 months ago by marongiu.luigi340
gravatar for Devon Ryan
9 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

Yes and I'm not sure who told you that it's best to reindex things on each machine. Simply make the index once and copy it. The copies will work perfectly fine. As you seem to have noticed, there are many precompiled indices out there. You can go ahead and use them without issue.

ADD COMMENTlink written 9 months ago by Devon Ryan86k

Good to know, thank you!

ADD REPLYlink written 9 months ago by marongiu.luigi340
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