Manifest files are used to import sequences into QIIME 2. They associate the sequence files with sample names and also give the location (directory) of the files to import. The beginning of a manifest file for importing paired reads looks like:
sample-id forward-absolute-filepath reverse-absolute-filepath EG10D100R2 /mnt/home/plate_1/EG10D100R2_16S_R1.fastq /mnt/home/plate_1/EG10D100R2_16S_R2.fastq EG10D100R3 /mnt/home/plate_1/EG10D100R3_16S_R1.fastq /mnt/home/plate_1/EG10D100R3_16S_R2.fastq EG10D25R1 /mnt/home/plate_1/EG10D25R1_16S_R1.fastq /mnt/home/plate_1/EG10D25R1_16S_R2.fastq
Single reads may also be imported using a manifest file that begins with something like:
sample-id absolute-filepath sample-1 $PWD/some/filepath/sample1_R1.fastq sample-2 $PWD/some/filepath/sample2_R1.fastq
I create manifest files in Excel by first importing a list of the forward files and moving them to the fifth column (column E). I then copy them to the next column (F) and substitute the portion of the file name designating tjhem as forward reads with one designating them as reverse reads. I put a list of corresponding sample names in column A. The sample names can often be extracted from the forward file names. I enter the path to the files in column D. For column B, I concatenate columns D and E, and for column C I concatenate columns D and F. Columns A, B and C must be copied and pasted as values so that they are no longer formulas. Then I delete columns D, E and F before inserting a header line with the sample IDs, forward and reverse absolute file paths.
I made a video to demonstrate my method.