Produce indivdual files - make.contigs with file parameter

To upload my sequences, for example to MG-RAST, I could really use the individual files. I generated paried end runs on the MiSeq. The make.contigs command with the file parameter (as per the SOP) produced a single fastaq file. I was wondering if I could run a similar command but where the outputs are the individual merged contig files? I have 747 samples so I would really like to avoid running a command like make.contigs(ffastq=test_1.fastq, rfastq=test_2.fastq) 747 times! I have the relevant stability.files file from when I ran the command in the SOP…

Any help is greatly appriciated.


The file option in the make.contigs command allows you to provide a group name. Then you can use the split.groups command to parse the file. For example:

F3D0 F3D0_S188_L001_R1_001.fastq F3D0_S188_L001_R2_001.fastq

split.groups(fasta=current, group=current)