fa2sina

This script does (1) sina search against arb file, (2) parse the output, and (3) make summary reports.

SINA program and ARB ribosomal database files are distributed by SILVA.

SINA for local installation
https://www.arb-silva.de/aligner/sina-download/
Source code of SINA is now publicly available (so it can be run on OSX now).
https://github.com/epruesse/SINA

ARB databases
https://www.arb-silva.de/download/arb-files/

Requirement:

SINA should be in PATH variable.

Usage:

fa2sina.pl fa=<fasta_file> arb=<arb_file> (lca=<0,1; default 1>) (lca_field=<lca field of arb; default tax_slv>) (out=<out; default fa.arb.fasta>)

Options:

fa: multiple fasta file
arb: arb file
lca: do lca tax assinment of sina or not
	default: 1 (do lca search)
lca_field: field of arb to be used for lca assignment
	default: tax_slv (for arb file of silva) can be self set field (e.g. tax_yh)
out: output fasta file
	default: <fa>.<arb>.fasta
	<out>.log_sina.txt for lca assigned result (parsed from the sina record in the header of each entry in the output fasta file)
	<out>.tax.txt: tab-separated file for entry and lca-assigned tax
	<out>.tax.summary.txt: summary of lca-assigned tax result
	<out>.tax.summary.ident.80.txt: summary of lca-assigned tax result
	<out>.tax.summary.ident.90.txt: summary of lca-assigned tax result
	<out>.tax.summary.ident.95.txt: summary of lca-assigned tax result
	<out>.arb.fa: ARB-compatible as pre-aligned sequences (gap characters at 5' and 3' ends are '.' insted of '-'. 

Note:

If you are just executing multiple fa2sina.pl simulutaneiously, check the arb file already has pt server.