Quake

[Gators]

Anyone use Quake with Ion Torrent data. I know it won't correct the indels, but thought I would see how it behaved anyway.

I get this error:

These reads must be longer than assumed. Increase the variable 'bitsize' in 'Read.h' to the read length.

Seems straightforward enough, except that I can't find the "Read.h" file anywhere. Nor is bitsize a documented option...

[rflrob]

Read.h is a source code file (specifically, a header file). When I download quake, there's both a "bin" directory (containing BINary executables), and a "src" directory, which is where Read.h is. If you edit it in there, that should do the trick, then from the command line run "make; sudo make install" (or, if this is on a computer run by someone else, talk to them about appropriate ways to install it).

I'd also note that Quake claims to be "specifically intended for Illumina sequencing reads", so here's a gun, there's your foot, have fun!

[Gators]

Ah yes, I saw that file shortly after I posted this...not sure where I was looking before when I claimed not to see it.

And for the record, yeah it doesn't really work...lost 30% of my reads, d'oh