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