nxtrim1

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Usage

nxtrim -1 R1.fastq.gz -2 R2.fastq.gz [options]

Program: nxtrim Version: v0.4.3 Contact: [email protected]

Unchanged in 2 releases since Debian 12 (Bookworm).

`-1 [ --r1 ] arg`	read 1 in fastq format (gzip allowed)
`-2 [ --r2 ] arg`	read 2 in fastq format (gzip allowed)

--justmp: just creates a the mp/unknown libraries (reads with adapter at the start will be completely N masked)

--rf: leave mate pair reads in RF orientation [by default are flipped into FR]

--preserve-mp: preserve MPs even when the corresponding PE has longer reads

--separate: output paired reads in separate files (prefix_R1/prefix_r2). Default is interleaved.

-s, --similarity arg (=0.85): The minimum similarity between strings to be considered a match (Hamming distance divided by string length)

-v, --minoverlap arg (=12): The minimum overlap to be considered for matching

-l, --minlength arg: (=21) The minimum read length to output (smaller reads will be filtered)

This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.

From nxtrim 0.4.3+dfsg-4 in Debian 13 (Trixie). Parsed by carta from the page's man source.