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mitool parse

Parse a given pattern in FASTQ file.




Input *.fastq or *.fastq.gz files. Use "{{n}}" if you want to concatenate files from multiple lanes.


my_file_L{{n}}_R1.fastq.gz my_file_L{{n}}_R2.fastq.gz
Output *.mic file.


--pattern <VALUE>
Pattern to parse against
--pattern-file <VALUE>
Load pattern from file
--preset <VALUE>
Load pattern and other options from built-in pattern library using a specific preset name, this also implies different default settings for other steps executed for the output file.
--threads <INT>
Number of processing threads
-u, --unstranded
If paired-end input is used, determines whether to try all combinations of mate-pairs or only match reads to the corresponding pattern sections (i.e. first file to first section, etc...)
-n, --limit <INT>
Limit number of reads
-b, --max-error-budget <FLOAT> (default: 10.0 or from preset)
Maximal bit budget, higher values allows more substitutions in small letters.
--unmatched <PATH>
File(s) to write reads that were not matched against the pattern. Specify this option the same number of times as there are input reads.
-r, --report <PATH>
Human readable report file. If file already exists, it will be overwritten.
-h, --help
Show this message and exit