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4.2 years ago
ATCG ▴ 370

I am interested in analyzing PacBio long read (full transcript) RNAseq data using GMAP; however, GMAP download page seems to have been removed. Does anyone know if GMAP is still available for download? PacBio have their own software SMRTlink software but I believe this will not run on windows or mac but only on Unix systems. Can anyone confirm this???

RNA-Seq GMAP PacBio • 1.9k views
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4.2 years ago
Carambakaracho ★ 3.1k

In case GMAT is a typo, GMAP and GSNAP can be found here:

http://research-pub.gene.com/gmap/

The PacBio SMRTLink suite runs perfectly fine on Linux, i believe it even requires Linux

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Thank you for your answer, Yes I am referring to GMAP. Let me clarify my second question: I only have a PC/Mac and no Unix server. Can I install SMRTLink on my Mac/PC??

Also, is GMAP a good alternative to SMRTLink? I need to detect gene isoforms without a reference.

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GMAP is only an alignment program where as SMRTlink is a suite of tools for working with PacBio data.

While official SMRTlink documentation clearly says this

SMRT Link server software cannot be installed on macOS® or Windows® systems.

You may be able to install SMRTlink on a Mac but it may not be worth the effort.

You should also look into minimap2 as an alternative alignment program.