trimΒΆ

$ micca trim --help
usage: micca trim [-h] -i FILE -o FILE [-w FORWARD [FORWARD ...]]
                  [-r REVERSE [REVERSE ...]] [-e MAXERATE] [-c] [-W] [-R]
                  [-f {fastq,fasta}]

micca trim trims forward and reverse primers from a FASTQ/FASTA file
using Cutadapt (doi: 10.14806/ej.17.1.200) internally. Primer and the
sequence preceding (for forward) or succeding (for reverse) it are
removed. Optionally, reads that do not contain the primers (untrimmed
reads) can be discarded with the options -W/--duforward and
-R/--dureverse. Recommended options are:

* always discard reads that do not contain the forward primer
  (-W/--duforward option);

* for overlapping paired-end (already merged) reads, also discard
  reads that do not contain the reverse primer (using both
  -W/--duforward and -R/--dureverse options).

IUPAC codes and multiple primers are supported.

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

arguments:
  -i FILE, --input FILE
                        input FASTQ or FASTA file (required).
  -o FILE, --output FILE
                        output FASTQ or FASTA file (required).
  -w FORWARD [FORWARD ...], --forward FORWARD [FORWARD ...]
                        trim forward primer(s). Only the best matching primer
                        is removed.
  -r REVERSE [REVERSE ...], --reverse REVERSE [REVERSE ...]
                        trim reverse primer(s). Only the best matching primer
                        is removed.
  -e MAXERATE, --maxerate MAXERATE
                        maximum allowed error rate (default 0.1).
  -c, --searchrc        search reverse complement primers too (default False).
  -W, --duforward       discard untrimmed reads (reads that do not contain the
                        forward primer) (always recommended) (default False).
  -R, --dureverse       discard untrimmed reads (reads that do not contain the
                        reverse primer) (suggested option for overlapping
                        paired-end already merged reads) (default False).
  -f {fastq,fasta}, --format {fastq,fasta}
                        file format (default fastq).

Examples

454 or Illumina single-end reads: trim forward primer and discard reads
that do not contain it. Moreover, trim reverse primer:

    micca trim -i input.fastq -o trimmed.fastq -w AGGATTAGATACCCTGGTA \
    -r CRRCACGAGCTGACGAC -W

Illumina overlapping paired-end (already merged) reads: trim
forward and reverse primers. Reads that do not contain the forward
or the reverse primer will be discarded:

    micca trim -i reads.fastq -o trimmed.fastq -w AGGATTAGATACCCTGGTA \
    -r CRRCACGAGCTGACGAC -W -R