NAME

n50.pl - A program to calculate N50 from FASTA/FASTQ files

AUTHOR

Andrea Telatin <andrea.telatin@quadram.ac.uk>

DESCRIPTION

This program parses a list of FASTA/FASTQ files calculating for each one the number of sequences, the sum of sequences lengths and the N50. It will print the result in different formats, by default only the N50 is printed for a single file and all metrics in TSV format for multiple files.

SYNOPSIS

n50.pl [options] [FILE1 FILE2 FILE3...]

PARAMETERS

-f, --format

Output format: default, tsv, json, custom. See below for format specific switches.

-s, --separator

Separator to be used in 'tsv' output. Default: tab. The 'tsv' format will print a header line, followed by a line for each file given as input with: file path, as received, total number of sequences, total size in bp, and finally N50.

-b, --basename

Instead of printing the path of each file, will only print the filename, stripping relative or absolute paths to it.

-j, --noheader

When used with 'tsv' output format, will suppress header line.

-n, --nonewline

If used with 'default' or 'csv' output format, will NOT print the newline character after the N50. Usually used in bash scripting.

-t, --template

String to be used with 'custom' format. Will be used as template string for each sample, replacing {new} with newlines, {tab} with tab and {N50}, {seqs}, {size}, {path} with sample's N50, number of sequences, total size in bp and file path respectively (the latter will respect --basename if used).

-p, --pretty

If used with 'json' output format, will format the JSON in pretty print mode. Example:

 {
   "file1.fa" : {
     "size" : 290,
     "N50" : "290",
     "seqs" : 2
  },
   "file2.fa" : {
     "N50" : "456",
     "size" : 456,
     "seqs" : 2
  }
 }

-h, --help

Will display this full help message and quit, even if other arguments are supplied.

COPYRIGHT

Copyright (C) 2017 Andrea Telatin

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.