micca-rarefy-seqsΒΆ

Rarefies a sequence file.

$ micca-rarefy-seqs --help
usage: micca-rarefy-seqs [-h] [-v] [-d DEPTH] [-f {fastq,fasta}] [-s SEED]
                         input output

micca-rarefy-seqs rarefies a sequence file.

positional arguments:
  input                 input fastq/a file
  output                output fastq/a file

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -d DEPTH, --depth DEPTH
                        number of sequences to retain (default 1000)
  -f {fastq,fasta}, --format {fastq,fasta}
                        input file format (default fastq)
  -s SEED, --seed SEED  random seed for the random generator (default 0)

Example:

 $ micca-rarefy-seqs seqs.fasta -f fasta -d 500

micca v. 0.1.
Author: Davide Albanese <davide.albanese@fmach.it>
Fondazione Edmund Mach, 2014.

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