ARGV

namespace: SMRUCC.genomics.Analysis.Metagenome.gast

gast -in input_fasta -ref reference_uniques_fasta -rtax reference_dupes_taxonomy [-mp min_pct_id] [-m majority] -out output_file

Methods

#ctor

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SMRUCC.genomics.Analysis.Metagenome.gast.ARGV.#ctor(Microsoft.VisualBasic.CommandLine.CommandLine)
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gast -in input_fasta -ref reference_uniques_fasta -rtax reference_dupes_taxonomy [-mp min_pct_id] [-m majority] -out output_file
Parameter Name Remarks
args -

Properties

db_host

-host, mysql server host name

db_name

-db, database name

full

-full, input data will be compared against full length 16S reference sequences [default: not full length]

in

input_fasta, input fasta file

m

[majority]

maj

-maj, percent majority required for taxonomic consensus [default: 66]

maxa

-maxa, [Optional] usearch –max_accepts parameter [default: 15]

maxr

-maxr, [Optional] usearch –max_rejects parameter [default: 200]

minp

-minp, [Optional] minimum percent identity match to a reference.
If the best match Is less Then min_pct_id, it Is Not considered a match
Default = 0.80

mp

[min_pct_id]

out

output_file, output filename

ref

reference_uniques_fasta, reference fasta file containing unique sequences of known taxonomy
The definition line should include the ID used In the reference taxonomy file.
Any other information On the definition line should be separated by a space Or a | symbol.

rtax

reference_dupes_taxonomy, reference taxa file with taxonomy for all copies of the sequences in
the reference fasta file
This Is a tab-delimited file, three columns, describing the taxonomy of the reference sequences
The ID matching the reference fasta, the taxonomy And the number Of reference sequences With this
this same taxonomy.

table

-table, database table to receive data

terse

-terse minimal output, includes only ID, taxonomy, and distance
See GAST manual For description Of other fields

udb

-udb, use a USearch formatted udb indexed version of the reference for speed.
(see http://drive5.com/usearch/manual/udb_files.html)

wdb

-wdb, use a USearch formatted wdb indexed version of the reference for speed.
[NO LONGER AVAILABLE with usearch6.0+]