segemehl_tool

[pari_89]

Has anyone tried to make use of segemehl. I am trying to compile it but each time getting an error like this:

libs/zran.o libs/zran.c
libs/zran.c:57:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [libs/zran.o] Error 1

Anyways, I would like a tool where I can map a Ion torrent technology reads of average 200 bp against a reference and view the alignments in a good viewer.

If anyone can provide an alternative to segemehl?

Thank you.

[GenoMax]

Has anyone tried to make use of segemehl. I am trying to compile it but each time getting an error like this:

libs/zran.o libs/zran.c
libs/zran.c:57:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [libs/zran.o] Error 1

Looks like you are missing the zlib library. Depending on what OS you are using the directions to install will be different.

Anyways, I would like a tool where I can map a Ion torrent technology reads of average 200 bp against a reference and view the alignments in a good viewer.

If anyone can provide an alternative to segemehl?

Thank you.

Have you tried new BWA-MEM algorithm in BWA?

See Heng Li's post here: http://www.biostars.org/p/67236/