Table 1.
Pipeline steps and associated outputs
| Step | Description | Major output |
|---|---|---|
| Initial processing | Primer (LROR/FLR2) and Illumina adaptor removal | Trimmed sequences |
| Visualize quality to determine sequence length cutoff | Quality plots | |
| Quality filter | DADA2 pipeline: filter, clean, and merge paired-end reads | ASV table and.fasta file |
| Pre-screening BLAST against AMF reference database | BLAST filtered ASV table and.fasta file | |
| OTU clustering | BLAST filtered OTU table and.fasta file | |
| Align sequences | Align reference and study sequences for forward (R1) and reverse (R2) reads | Forward and reverse.fasta alignments |
| Concatenate forward and reverse alignments | Concatenated.fasta alignment | |
| Tree building | Place study sequences (in batches) into backbone reference tree | RAxML trees |
| Extract AMF | Extract sequences in the Glomeromycota clade | Glomeromycota clade filtered OTU or ASV table and.fasta file |
| Extract AMF families | Extract sequences within each of the 11 Glomeromycota family clades | Family clade filtered OTU or ASV tables and.fasta files |