nast-ier(1)

Overview

The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences.

The alignment algorithm involves global dynamic programming profile alignment to fixed (NAST-formatted) multiply aligned template sequences without any end-gap penalty.

NAST-iEr is part of the microbiomeutil suite.

Options

Required:

--query_FASTA: query database in FASTA format (seqs to NAST-align)

Optional: (unless defaults are not set!)

--db_NAST: reference database in NAST format (default: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta)

--db_FASTA: reference database in FASTA format (default: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta)

--num_top_hits: number of top hits to use for profile-alignment (default: 10)

--Evalue: Evalue cutoff for top hits (default: 1e-50)

Releases

Unchanged in 6 releases since Debian 8 (Jessie).

8–13