micca-preprocΒΆ

$ micca-preproc --help
usage: micca-preproc [-h] [-v] [-f PRIMER] [-r PRIMER] [-e RATE] [-O LENGTH]
                     [-q QUALITY] [-l LENGTH] [-o DIR]
                     input [input ...]

micca-preproc performs several preprocessing steps on 454/Illumina amplicon
sequencing data:

 - primer trimming both in the 5' and 3' ends of reads using
   semi-global alignments
 - quality trimming using sliding windows
 - ending Ns trimming
 - minimum length filtering

positional arguments:
  input                 input fastq file(s)

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -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-threshold QUALITY
                        threshold for trimming based on average quality in a
                        window (default 20)
  -l LENGTH, --length-threshold LENGTH
                        threshold to keep a read based on length after
                        trimming (default 200)
  -o DIR, --output-dir DIR
                        output directory (default preprocessed)

Example:

 $ micca-preproc *.fastq -f AGGATTAGATACCCTGGTA -r GTCGTCAGCTCGTGYYG -O 10

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

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