merge sff files

Commands in mothur
1

Hi, I was wondering which command can merge multiple “sff” files.

Thanks

2

http://www.mothur.org/wiki/Merge.files

3

Hi Pat,

I read that link before I posted the question. It says using sfffile? Is it a mothur command? If it is not, where I can download the tools.

Thanks

4

You’ll have to get sfffile from 454 or your sequence provider. It’s not a mothur command.

5

if you want to merge sff files you need to contact your 454 regional so called “software trainer”. He/she will send you a link to download a software package that comes with one of their instruments (GS_Junior_Software). This packages contained 5 different software programs. You need to install two of them, the DataAnalysis and DataProcesing Packeges. The installation has to be done on a CentOS or Red Hat. I did mine on a CentOS i386 (won’t work on 64) in a virtual machine (VirtualBox). Next, you need to locate the SFFFILE executable and move it to where you have your SFF files.
i copied the command into Documents/454 in the virtual machine

cd 454
chmod a+x sfffile.exe
./sfffile -o combined.sff file1.sff file2.sff
after all, my VM ran out of memory (although i assigned 7 G of RAM to the VM on a McBookPro)
i did the same exercise on a Linux server running tonnes of RAM and still ran out of memory.
i believe the problem was that one of my files was too big to be merged.
sfffile works but has its limitations.
it’s ideal to contact the sequencing centre who processed your samples.