mitool parse

Parse a given pattern in FASTQ file.

Usage:

mitool parse [OPTIONS] [SOURCE]... DESTINATION

Arguments:

<SOURCE>

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

<DESTINATION>

Output *.mic file.

Options:

--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