statsΒΆ

$ micca stats --help
usage: micca stats [-h] -i FILE [-o DIR] [-n TOPN]

micca stats reports statistics on reads in a FASTQ file. micca stats
returns in the output directory 3 tab-delimited text files:

* stats_lendist.txt: length distribution;
* stats_qualdist.txt: Q score distribution;
* stats_qualsumm.txt: quality summary. For each read position, the 
  following statistics are reported:
  - L: read position;
  - NPctCum: percent of reads with at least L bases;
  - QAv: average Q score at position L;
  - EERatePctAv: average expected error (EE) rate %.

Moreover, micca stats returns the respective plots in PNG format,
stats_lendist_plot.png, stats_qualdist_plot.png, and 
stats_qualsumm_plot.png.

optional arguments:
  -h, --help            show this help message and exit

arguments:
  -i FILE, --input FILE
                        input FASTQ file, Sanger/Illumina 1.8+ format
                        (phred+33) (required).
  -o DIR, --output DIR  output directory (default .).
  -n TOPN, --topn TOPN  perform statistics only on the first TOPN sequences
                        (disabled by default).

Examples

Compute statistics on the top 10000 sequences of input.fastq:

    micca stats -i input.fastq -o stats -n 10000