micca-preproc-checkΒΆ

Tries different combinations of length and quality thresholds.

$ micca-preproc-check --help
usage: micca-preproc-check [-h] [-v] [-F FORMAT] [-f PRIMER] [-r PRIMER]
                           [-e RATE] [-O LENGTH] [-q QUALITY [QUALITY ...]]
                           [-l LENGTH [LENGTH ...]]
                           input output

micca-preproc-check tries different combinations of length and
quality thresholds.

positional arguments:
  input                 input fastq file(s)
  output                output image filename.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -F FORMAT, --format FORMAT
                        output image formatfile (png, pdf, ps, eps, svg)
                        (default png)
  -f PRIMER, --primer-forward PRIMER
                        remove forward primer sequences and discard untrimmed
                        reads
  -r PRIMER, --primer-reverse PRIMER
                        remove reverse primer sequences
  -e RATE, --primer-error-rate RATE
                        maximum allowed error rate (number of errors divided
                        by the length of the region) (default 0.1)
  -O LENGTH, --primer-overlap LENGTH
                        minimum overlap length. If the overlap between the
                        read and the primer is shorter than LENGTH, the read
                        is not modified (default 10)
  -q QUALITY [QUALITY ...], --quality-threshold QUALITY [QUALITY ...]
                        thresholds for trimming based on average quality in a
                        window (default [10, 20, 25, 30])
  -l LENGTH [LENGTH ...], --length-threshold LENGTH [LENGTH ...]
                        thresholds to keep a read based on length after
                        trimming (default [50, 100, 150, 200, 250, 300, 350,
                        400, 450, 500, 550])

Example:

 $ micca-preproc-check *.fastq preproc.png -f AGGATTAGATACCCTGGTA -r GTCGTCAGCTCGTGYYG

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

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