nuget
gast -in input_fasta -ref reference_uniques_fasta -rtax reference_dupes_taxonomy [-mp min_pct_id] [-m majority] -out output_file
ARGV
01 Syntax
SMRUCC.genomics.Analysis.Metagenome.gast.ARGV
02 Methods
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| in | 1 | input_fasta, input fasta file |
| ref | 1 | 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. |
| rtax | 1 | 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… |
| mp | 1 | [min_pct_id] |
| m | 1 | [majority] |
| out | 1 | output_file, output filename |
| full | 1 | full, input data will be compared against full length 16S reference sequences [default: not full length] |
| maj | 1 | maj, percent majority required for taxonomic consensus [default: 66] |
| maxr | 1 | maxr, [Optional] usearch --max_rejects parameter [default: 200] |
| maxa | 1 | maxa, [Optional] usearch --max_accepts parameter [default: 15] |
| minp | 1 | minp, [Optional] minimum percent identity match to a reference. |
| wdb | 1 | wdb, use a USearch formatted wdb indexed version of the reference for speed. |
| udb | 1 | udb, use a USearch formatted udb indexed version of the reference for speed. |
| terse | 1 | terse minimal output, includes only ID, taxonomy, and distance See GAST manual For description Of other fields |
| db_host | 1 | host, mysql server host name |
| db_name | 1 | db, database name |
| table | 1 | table, database table to receive data |
04 Members
#ctor(
CommandLine) gast -in input_fasta -ref reference_uniques_fasta -rtax reference_dupes_taxonomy [-mp min_pct_id] [-m majority] -out output_fileParameters
| Name | Type | Description |
|---|---|---|
args | CommandLine | - |
in
input_fasta, input fasta file
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.
mp
[min_pct_id]
m
[majority]
out
output_file, output filename
full
-full, input data will be compared against full length 16S reference sequences [default: not full length]
maj
-maj, percent majority required for taxonomic consensus [default: 66]
maxr
-maxr, [Optional] usearch --max_rejects parameter [default: 200]
maxa
-maxa, [Optional] usearch --max_accepts parameter [default: 15]
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
wdb
-wdb, use a USearch formatted wdb indexed version of the reference for speed. [NO LONGER AVAILABLE with usearch6.0+]
udb
-udb, use a USearch formatted udb indexed version of the reference for speed. (see http://drive5.com/usearch/manual/udb_files.html)
terse
-terse minimal output, includes only ID, taxonomy, and distance See GAST manual For description Of other fields
db_host
-host, mysql server host name
db_name
-db, database name
table
-table, database table to receive data
ToString()