Chao1.pl
Takes a table of OTU abundance in one or more samples and calculates the chao1 index (with 95% Confidence Interval) for each sample. To use it with Qiime OTU Tables, run it ignoring 1 left column and with header.
See source code, Artistic license 2.0.
§ References
Chao, 1984, Scandinavian J Stat; Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
- Perl.
§ Usage
Chao1.pl -i in_file [opts] > out_file
§ Arguments
- Input file*
-i in_file
Input table (columns:samples, rows:OTUs).- Rows
-r integer
Number of rows to ignore.- Left columns to ignore
-c integer
Number of columns to ignore.- Right columns to ignore
-C integer
Number of columns to ignore at the end.- Delimiter
-d string
Delimiter between columns.Supported escaped characters are: \t (tabulation), and \0 (null bit).- Header
-h
If set, the first row is assumed to have the names of the samples.- Output file*
out_file
Chao1 index and 95% CI bounds for each sample, in tab-delimited format.