nuget
compares trimmed sequences against a reference database for assigning taxonomy, reads a fasta file of trimmed 16S sequences, compares each sequence to a Set Of similarly trimmed ( Or full-length ) 16S reference sequences And assigns taxonomy
GastAPI
01 Syntax
SMRUCC.genomics.Analysis.Metagenome.gast.GastAPI
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| Invoke | 2 | bash gast -in input_fasta -ref reference_uniques_fasta -rtax reference_dupes_taxonomy [-mp min_pct_id] [-m majority] -out output_file |
| assign_taxonomy | 1 | get dupes from the names file and calculate consensus taxonomy |
| load_reftaxa | 1 | Get dupes Of the reference sequences And their taxonomy |
| parse_uclust | 1 | Parse the USearch results And grab the top hit |
03 Properties
04 Members
Invoke(ARGV)
reads a fasta file of trimmed 16S sequences, compares each sequence to a set of similarly trimmed ( Or full-length ) 16S reference sequences And assigns taxonomy
Parameters
| Name | Type | Description |
|---|---|---|
args | ARGV | - |
Invoke(
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 | - |
assign_taxonomy(
StreamWriter, String, Dictionary(Of String, String()()), Dictionary(Of String, String()), Double, Boolean, String)get dupes from the names file and calculate consensus taxonomy
Parameters
| Name | Type | Description |
|---|---|---|
names_file | StreamWriter | - |
results_ref | String | - |
ref_taxa_ref | Dictionary(Of String, String()()) | - |
load_reftaxa(
String)Get dupes Of the reference sequences And their taxonomy
Parameters
| Name | Type | Description |
|---|---|---|
tax_file | String | - |
parse_uclust(
String, Boolean, Boolean, Boolean, Int32)Parse the USearch results And grab the top hit
Parameters
| Name | Type | Description |
|---|---|---|
uc_file | String | - |
usearch
mothur
verbose