From: A comprehensive evaluation of multicategory classification methods for microbiomic data
Parameter | Value | Description |
---|---|---|
otu picking method | uclust | uclust, creates ‘seeds’ of sequences which generate clusters based on percent identity. |
clustering algorithm | furthest | Clustering algorithm for mothur otu picking method. Valid choices are: furthest, nearest, average. |
max cdhit memory | 400 | Maximum available memory to cd-hit-est (via the program’s -M option) for cdhit OTU picking method (units of Mbyte) |
refseqs fp | None | Path to reference sequences to search against when using -m blast, -m uclust_ref, or -m usearch_ref |
blast db | None | Pre-existing database to blast against when using -m blast |
similarity | 0.97 | Sequence similarity threshold (for cdhit, uclust, uclust_ref, or usearch) |
max e value | 1.00E-10 | Max E-value when clustering with BLAST |
prefix prefilter length | None | Prefilter data so seqs with identical first prefix_prefilter_length are automatically grouped into a single OTU |
trie prefilter | FALSE | Prefilter data so seqs which are identical prefixes of a longer seq are automatically grouped into a single OTU |
prefix length | 50 | Prefix length when using the prefix_suffix otu picker |
suffix length | 50 | Suffix length when using the prefix_suffix otu picker |
optimal uclust | FALSE | Pass the -optimal flag to uclust for uclust otu picking. |
exact uclust | FALSE | Pass the -exact flag to uclust for uclust otu picking. |
user sort | FALSE | Do not assume input is sorted by length |
suppress presort by abundance uclust | FALSE | Suppress presorting of sequences by abundance when picking OTUs with uclust or uclust_ref |
suppress new clusters | FALSE | Suppress creation of new clusters using seqs that don’t match reference when using -m uclust_ref or -m usearch_ref |
suppress uclust stable sort | FALSE | Do not pass -stable-sort to uclust |
max accepts | 20 | Max_accepts value to uclust and uclust_ref |
max rejects | 500 | Max_rejects value to uclust and uclust_ref |
word length | 12 | W value to usearch, uclust, and uclust_ref. Set to 64 for usearch. |
stepwords | 20 | Stepwords value to uclust and uclust_ref |
suppress uclust prefilter exact match | FALSE | Do not collapse exact matches before calling uclust |