make.contigs and 'clean' data

Hey Pat,

I have been given a set of ‘clean’ Illumina sequencing reads that I need to analyze but I’m not sure how to get started. With this data I have one .fna file per sample in which the forward and reverse reads have already been joined and there is no quality data. Is there a way to skip the option to merge the reads but still combine the data from all samples?



You can use the command to get the appropriate group file, then just concatenate your individual fasta files into a single one. From there you can pretty much start the SOP as normal.

mothur >, groups=A-B-C, output=merge.groups)
mothur > system(cat A.fna B.fna C.fna > merge.fasta)

mothur > unique.seqs(fasta=merge.fasta)
mothur > count.seqs(name=merge.names, group=merge.groups)

Would give you the fasta/count_table files for everything downstream.