Running MiSEQ SOP starting with alignment step?

Is there any way to start the MiSEQ SOP after the make.contigs step? Some data we received from a sequencing facility is proving problematic, but we do have an assembled set of the reads that they provided as a fasta. The sequence do still have the barcode at the 5’ end in this fasta, but I’m just not sure how to proceed - I’m used to having the individual reads for each sample, and that wasn’t provided. I’ve tried concatenating all of the forward runs into one fastq and all of the reverse runs into another, and was able to parse those out into the individuals samples, and thought that this would then let me do make.contigs as usual, but I keep running into the error where a sequence in the forward fastq isn’t present in the reverse fastq - so I’d like to try starting with what I think is at least usable data - the fasta. But I’m not sure how to proceed…any help appreciated.

We find that most assemblies are pretty poor relative to what you get from make.contigs. Regardless, you’d have to write your own script or use trim.seqs to remove the distal barcode.