Documentation read from 04/17/2019 22:07:28 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_summarize_contigs.



    svr_summarize_contigs <genome_ids.tbl >genome_data.tbl

For each incoming genome ID, return statistics about its contigs.

This script takes as input a tab-delimited file with genome IDs at the end of each line. For each genome ID, a single output line is produced containing statistics about the genome's contigs.

This is a pipe command: the input is taken from the standard input and the output is to the standard output.

The data fields produced for each genome (and which are appended to each output line in this order) are as follows:

  1. number of contigs
  2. mean contig length
  3. median contig length
  4. total number of base pairs
  5. total number of ambiguity characters
  6. total number of GC pairs

Command-Line Options


The URL for the Sapling server, if it is to be different from the default.


Column index. If specified, indicates that the input IDs should be taken from the indicated column instead of the last column. The first column is column 1.